Ilya Nemenman: Theoretical Biophysics @ Emory - User contributions [en]

Physics 434, Lecture 1 additional notes

2022-01-19T14:11:36Z

Ilya:

{{PHYS434-2016}}

You should carefully read the course [[Physics 434, 2016: Syllabus| Syllabus]] for the class details. Briefly, the following are the key points.

This is a mathematical / computational course, akin to a typical upper division physics course. While hard, the course will quite doable for most of you, with sufficient effort. To help, we will schedule regular office hours and review sessions as needed. You should be working in groups, but the eventual write-ups of homeworks and project reports should be done individually. The students in the class will consist of different groups, including physics majors, biology majors, and some graduate students. We will try to use the language of computer simulations to bring all of you together to the same page. None of you are probably experts in programming, but this is OK, as you will learn during the class. Those students registered for the 534 version of the class will have additional/harder homework assignments, to justify the difference in the course number. The course has a somewhat nontraditional grading policy, including homework problems, one in-class exam, and project work and reports. Please see details in the [[Physics 434, 2016: Syllabus| Syllabus]]. Homework assignments will be distributed on about Wednesdays, and they will be due by end of the day on the Fridays one week later. Starting mid-October, you will also be working on your projects, to be presented in class in December.

===What is this class about?===
This is a class about physics of living systems. At the first glance, using the words ''physics'' and ''life'' in one sentence is contradictory. Indeed, physics is about simple mathematical models of the underlying processes, about general understanding. It is about theories that find unanticipated connections among seemingly unconnected parts of the natural world, such as a ferromagnet and a water-to-vapor transition, or the Higgs boson and properties of engineered materials. In contrast, modern biology is traditionally represented as not accepting theories (beyond maybe the evolutionary theory of Darwin). Every detail matters. A cell surface receptor molecule will behave very differently depending on which cell it is on. A cell with the same genome will behave very differently, and may differentiate into different fates, depending on where in the organism it is. The same organism may respond quite differently to the same stimulus, sometimes choosing to completely ignore it. Why is it that we hope that there will exist physics in living systems?

All of you have taken sufficient number of biology classes. So if I ask you to name some important biological discoveries in the 20th century (e.g., some physiology/medicine Nobel prizes), you can probably name a few. You will probably name the Watson-Crick discovery of the structure of DNA as one of the most important of these biological discoveries, at least in the context of molecular/cellular biology. If I ask you to dig deeper into your memory, and nominate a few other discoveries, then very soon you will mention the Hodkin-Huxley model of action potential generation in neurons as maybe the greatest discovery ever made in neurobiology. And then very soon someone will nominate the Luria-Delbruck experiment, which has discovered that natural selection acts on pre-existing variation in the population, rather than causing new variation, as the most important Nobel in the context of evolutionary and population biology.

What do all three of these discovered have in common? They all were made by a pair of scientists, where the first was an experimental biologist, and the second was a theoretical physicist/applied mathematician. In fact, it seems that theory, and more specifically physics style theory, is a lot more common in biology than we are led to believe. One can naively say that it is because all biological systems are made of molecules, which are physical objects that obey physical laws. This is true, but it is only part of the story. As the three examples above show, physics exists in biology at every level, from molecules, to cells, organisms and populations. We will see a lot more examples of this as we dive deeper into the class.

What allows this to happen is that seemingly disparate biological phenomena are, in fact, much closer related to each other than one may naively hope for. The rules of chance ensure that an ''E. coli'' trying to figure out where food is based on activity of its surface receptors that bind various food source molecules needs to solve a problem similar to what a fly's brain needs to solve when it tries to estimate its own self-motion through the world based on the activity of its visual neurons, or the problem that we, as scientists, are solving when we are learning about the ''E. coli'' from our experiments. This is what this class is about -- we will identify some problems that biological systems need to solve in the course of their lives, understand their physical structure, and then see what are the limitations imposed by this physical structure, independent of the details of the organism that is trying to solve the problem. In other words, we will try to focus on things that truly matter, and to build broad theories of phenomena, rather than their narrow, focused models.

We cannot embrace the unembraceable, and so, we will only be building these theories in a few specific examples. We will start with models of cellular dynamics, and then switch to questions of information processing in biology, where we will ask and answer:
*'''How well, in objective terms, do various biological systems transduce available sensory information?'''
*'''What stays in the way of their performance?'''
*'''Which strategies can be used by the systems to improve the quality of processing?'''

Before we leave this introduction, we still need to answer one more question: why numbers? That is, why such a focus on mathematics? Here the answer is very simple -- to see if we understand the world, we need to make a prediction, and then test it experimentally. Testing involves comparison of predictions to the observations. However, the only things we know how to compare are numbers. Think about it carefully: the only thing we can compare are numbers! Thus the language of any science, including biology, is mathematics. One can then ask if one wants to compare trends, which are basically binary numbers (e.g., up or down), or if one wants to predict, measure, and compare real-valued numbers like we normally do in physical sciences. A binary experiment gives us, at best, one bit of information (we will formalize this later in the class), and hence can rule out, at best, half of theories. Real-valued predictions have more discriminatory power, and are thus a lot more valuable. We will stick to them in this class.

==Introducing the model systems==
''This is a carryover from the earlier incarnation of the class. Worth reading, and we will return to these systems later in the course of the semester.''

Theories rarely emerge directly on a piece of paper, out of nothing. They come from studies of specific experimental systems. In this class, we will introduce a series of such models systems. While many will appear for just a few lectures, some of the model systems will persist through most sections of the class. In the context of cell biology, our main hero will be the ''E. coli'' cell, and specifically its chemotactic behavior. For evolutionary questions, we will again focus on "E. coli", but this time on response of their populations to stresses, such as antibiotics and bacterial viruses. For neuroscience, we will focus on visual signal transduction. And finally, for behavior, we will explore foraging in rats.

===Introduction to ''E. coli'' chemotaxis===
So let's introduce our heroes, starting with the smallest, the ''E. coli''

''E. coli'' is a small cell about <math> 1\mu m</math> in linear dimensions. It's a natural measuring stick for cellular biology. Read more about the organism in the [[media:sizing-up-e-coli.pdf | Sizing up E coli]] section in ''Physical Biology of the Cell''. As every bacterium, ''E. coli'' has no internal organelles, such as nucleus, and it is basically a bag of molecules: DNA, RNA, proteins, and smaller metabolites, all packed rather densely and semi-regularly. ''E. coli'' spends at least a part of its life swimming around trying to find nutrients, then eating them, growing, and dividing (they can also grow as parts of biofilms or colonies, but we will not focus on this).

The swimming behavior of ''E. coli'' is rather intricate, as illustrated by now-classic movies from the Howard Berg lab, http://www.rowland.harvard.edu/labs/bacteria/movies/showmovie.php?mov=fluo_bundle. The bacterium is pushed forward by a bundle of flagella that rotate. Such smooth forward motion is called the run. Once in a while, the flagella bundle breaks apart, and the bacterium tumbles and reorients instead of going smoothly forward. We will spend a lot of time studying this system. In particular, you can look up the basic chemical diagram of the process at http://www.rowland.harvard.edu/labs/bacteria/projects/fret.php. However, now let's ask the question: why does ''E. coli'' do what it does? Why running and tumbling? Answering this question will be our first ''aha!'' moment -- we can understand a lot about biology by studying basic physical principles!

So the ''E. coli'' wants to go where life is greener. But how does it know where it's greener? To see where pizza is, you can look around, you can smell. The bacterium can do nothing of this. It can only count molecules of chemicals that it cares about, and go to where there are more of such molecules. Experiments tell us (Adler 1975, Budrene and Berg, 1991, 1995) that ''E. coli'' can find maxima of nutrient concentrations even when concentrations are as small as 1 nM. What does it mean in more reasonable units?
<math>1{\rm M}=\frac{N_A}{1 {\rm l}}\approx \frac{6 \cdots 10^{23}}{10^{-3} {\rm m}^3}=6\cdot 10^{26}{\rm m}^{-3}</math>

Thus <math> 1{\rm nM}\approx 6\cdot 10^{17}{\rm m}^{-3}</math>. On the other hand, ''E. coli'' is roughly speaking a cylinder, of a diameter of about <math>r=700 {\rm nm}</math> and the height of about <math>h=3 \mu{\rm m}</math>. Its volume is then <math> V= \pi r^2h=1.2 \cdot 10^{-18} {\rm m}^3</math>. Thus at 1 nM concentration, there are only about <math> 1.1 \cdot 10^{-18} {\rm m}^3 \times 6\cdot 10^{17}{\rm m}^{-3}\approx 0.7\approx 1</math> molecule of the nutrient in the entire ''E. coli'' volume. How can then the bacterium know where the grass is greener, when it only has total of 1 molecule to count? (This is a bit at the extreme of ''E. coli'' sensitivity, but it's important to be dramatic!)

The worst part about numbers so small is that they are also random. Molecules diffuse around (we will talk about Brownian motion a lot more later in the class). Thus if one has one molecule of food around, one can also have two, or zero, or three. Or even (with quite a bit lower probability) seven. Comparing numbers that are so small, and with fluctuations so large, is impossible. The only solution is to get more molecules. And this requires to capture them from a larger volume. There are, roughly speaking, three ways of doing so. One possibility is to stir the environment (and we have talked briefly about this in class), the second is to stay in place for a long time and to wait till more molecules diffuse one's way, and the third possibility is to run and hence to scoop molecules from a larger volume. We will talk more about properties of diffusion later -- but, roughly speaking, waiting is not very efficient -- it will take very long time for new molecules to arrive in the vicinity of the cell by diffusion. This leaves stirring and running, and ''E. coli'' chooses to run.

'''Grad Students''' (later denoted as ''' ''GS'' '''): Let's calculate how long one would need to wait to get a certain accuracy in determining the concentration around oneself. The accuracy of the concentration estimation is proportional to the accuracy in counting molecules, so that <math>\delta c/c=\delta n/n</math>. But molecules come and go randomly, forcing Poisson statistics of arrivals, so that <math>\delta^2 n = n</math>. At the same time, the average number of molecules in a volume of the bacterium is <math>Vc</math>, where the volume is, roughly speaking, the cube of its linear dimension, <math>V\sim a^3</math>. Combining these, we get <math>\delta c/c= 1/\sqrt{ca^3}</math>. If the ''E. coli'' can wait for a long time <math>T</math> then it can do <math>N=T/\tau</math> observations, where <math>\tau</math> is the duration of a single observation. This results in the usual square root decrease in the variance, so that <math>\delta c/c\sim 1/\sqrt{ca^3T/\tau}</math>.

Now, what is <math>\tau</math>? If we measured molecules once, they are going to stick around, and remeasuring them again soon is useless -- we are not making an independent measurement! One needs to wait while the old molecules diffuse away, and the new ones diffuse in. For a cell with the linear size of <math>a</math>, it will take about <math>\tau\sim a^2/D</math> for this to happen, where <math>D</math> is the diffusion coefficient. Combining the two equations, results in <math>\delta c/c\sim 1/\sqrt{cDa^3T/a^2}= 1/\sqrt{cDaT}</math>. This is the celebrated Berg-Purcell limit in concentration sensing. Note a peculiar scaling, which is the results of the two-dimensional nature of diffusion (we will discuss what this means in later classes): the accuracy increases as a square root of the ''linear'' size of the cell. It also increases as a square root of time. Thus waiting in one spot, or growing bigger, is not a very effective strategy for improving concentration session. '''End ''GS''.'''

By running, a bacterium is able to sweep molecules in a larger volume, roughly proportional to its cross section, times the length of the run (which is, in its turn, a product of the velocity and the run time), so that the number of captured molecules is <math>n\sim ca^2vT</math>. For the run to make sense, it must be long enough to not only produce <math>n\gg1</math>, but also to ensure that more molecules are picked up by running, than simply by waiting. This sets the smallest time <math>T</math> of a second or so that the bacterium must run (we are skipping a few steps here), if it runs with the velocity of about 20 microns/sec. It needs to run long enough to outrun diffusion! On the other hand, the bacterium cannot run straight for long (for longer than about 10s), because random hits by water molecules will make it change its direction by this time. Indeed, the bacterium in real life runs for about ~5 seconds before turning.

In conclusion, ''E. coli'' lives in a weird world: it must count individual molecules of chemicals to know where to go, and these numbers are small (it also lives in the world where masses are not important, as we will show in a homework problem). Its behavioral strategy is fully dictated by the physical structure of the world it leaves in: small size that limits total number of molecules in the cell volume, diffusion that takes molecules to and away from the cell and prevents the bacterium from keeping moving in a straight line, and the need to go to greener pastures.

''E. coli'' life is probabilistic, weird, but quite understandable!

===Introduction to visual neural computation===

We've just convinced ourselves that, for ''E. coli'', the world is probabilistic, and every single molecule of a signal matters. But the bacterium is small, and we are big. It seems that the randomness should be a lot less important for us. Indeed, some times it is less important -- if I want to go to an office door, I can mostly make it without random jitter, at least on large scales (though a lot of work is being done nowadays on studying randomness of individual motor responses). But in the sensory domain, it turns out that small numbers, and the associated randomness, often matter even for animals as big as us. So let's consider this in the context of neural computation in vision.

For the purpose of this class, neurons will be rather simple devices (see Dayan and Abbott, 2005). They collect electrical currents produced by neurons that are connected to them through synaptic connections. They discharge those collected charges (and hence lower their voltage) through the membrane, just like an RC circuit you studied in intro physics does. And when the voltage finally goes above a certain threshold in this tug of war between synaptic inputs and membrane discharge, the neurons spike -- they produce an impulse, an action potential, that travels through the axon of the neuron and feeds into the other neurons through their synapses. In vertebrate retina, the first set of cells, the photoreceptors (the rods and the cones) actually don't spike, but we will disregard this complication for now, till we study these cells in much detail in the third quarter of the class.

Because the number of input neurons is large, and they all fire at random times, the firing pattern of a single neuron is not deterministic either. Spikes occur at random time points, and a typical neuron may produce anywhere from ~100-200 spikes per second (for a visual neuron in an insect), to maybe 20-60 spikes in cells in the primary visual cortex of a monkey, to barely a spike a second or even less for neurons in other areas of our cortex. Some of the most interesting questions in today's neuroscience are about how important this randomness is for representing the information about the outside world, and we will study some of this later in the class (Rieke et al, 1999).

For now, just notice that we often can make decisions after being exposed to a visual image for ~200ms, and insects, whose vision is faster than ours, can make decisions in ~20ms or so. Let's take 100ms as a typical decision time for our current arguments. Thus a cell in our retina, a pixel that is measuring the brightness at some point of the visual world, even if it fires at a rate of 100 spikes per second, will only produce about <math> \sim 100 {\rm spikes/s} \times 100 {\rm ms}=10 {\rm spikes}</math> before the cell in the next level of our brain must make a decision about the level of brightness that is being seen. Our neural cells have about as many spikes to count as ''E. coli'' have molecules to count before choosing where to go! Yes, we have many neurons, and we should be able to use their collective activity to guide our decision processes, but this doesn't change the fact that our neural computation is fundamentally probabilistic, with small number of spikes. And the design of the brain must somehow make this all work.

In fact, the problem of randomness in our eyes starts even earlier, all the way at photon capture. As one of the homework problems will show, even in bright light, a single photoreceptor in our eyes collects not much more than ~1000 photons during the typical reaction time of ~100 ms. When we move into a dim environment of a badly lit room, or the world half an hour after the sunset, our photoreceptors may be capturing ~1 photon per photoreceptor, and we can detect dim light flashes as small as ~10 or fewer photons falling on our entire retina (Bialek, 2013). So, even the neural computation aside, sensing in even large organisms as us, is also fundamentally probabilistic.

===Main point to carry out===
In both of these examples, and in the others that we will discuss later, a major complication standing in front of biological organisms is chance. A molecule of a nutrient may be there or not, photon may arrive or not, and spikes may be there or not. '''Biological signal processing is not deterministic''' -- randomness is important, and it must be dealt with, or leveraged, but it cannot be ignored. Hence randomness will be the thread that will connect all of the components of this course, and we will spend the first half of the course introducing mathematical and computational tools to study randomness in biology, and building up the necessary intuition.

Physics 190, 2015: Freshman Seminar: Where do laws of nature come from?

2020-11-24T17:47:40Z

Ilya: /* Reading */

{{PHYS190-2015}}

We will talk about what we mean by such different terms as laws of nature, theories, principles, and models. We will discuss why we believe that there should be laws describing how nature works, whether traditional inanimate nature, or biological and even social systems. We will investigate why and how such laws would emerge, and why they will be written always in the language of mathematics.

We will address these questions from the perspective of many different fields: physics, biology, philosophy, etc. Nonetheless, this is a physics class, a science class, and not a philosophy class (I am quite ill-equipped to teach philosophy). Thus we will deal with philosophy in general, and philosophy of science in particular, only tangentially. We will not argue much about whether the reality is fundamentally mentally-constructed, immaterial, and subjective, or objective, and exists independently of us talking about it. Instead, we will focus on how science describes this reality, largely leaving the nature of the reality undiscussed, and taking approaches that a practicing scientist would use.
*What are scientific laws?
*Why does Nature allow itself to be confined by laws?
*How do we discover these laws?
Additionally, we will be attending a handful of science seminars across campus, trying to reconcile what we learn during the seminar with what real scientists are doing.

==News==
*We had to reschedule the second replacement class again. The two extra classes now are '''Mar 20, 11:30-12:45''' and '''Mar 24, 8:45-10:00'''.
*Replacement classes have been scheduled for '''Mar 20, 11:30-12:45''' and '''Mar 27, 11:30-12:45'''.
*Two classes are being rescheduled. '''Please pay particular attention to assignment due dates and new class times.''' I will be updating the schedule as it becomes clearer, after you submit your availability. [[User:Ilya|Ilya]] 15:34, 25 February 2015 (EST)
*A discussion board has been setup for the class on Blackboard. Please use it to share and discuss your ideas.[[User:Ilya|Ilya]] 21:14, 25 January 2015 (EST)
*Welcome to the class!

==Logistics==
*[[Physics 190, 2015: Syllabus|Syllabus]] -- we will deviate from it in the course of the class
*[[Physics 190, 2015: Discussion Leaders|Discussion Leaders]] -- what you are expected to do
*Weekly office hours: Monday, 2:00-3:00.

==Schedule==
#'''January 14'''. Introduction.
#: No reading assignment.
#: Attending seminar: Tatyana Sharpee, [http://www.quantitative.emory.edu/events/speakerseries1.html Maximally Informative Behaviors Implemented by Simple Neural Circuits]
#'''January 19'''. Holiday, no class.
#'''January 21'''. Laws of nature, scientific principles, scientific theories, models in sciences, hypotheses.
#:''Assignment'': Research, make, and submit your written definition of the five concepts above, and be ready to discuss them. It may help you to start from the encyclopedia articles below, and then maybe to follow citations to primary sources.
#:''Additional topics'': We will discuss the past seminar by Sharpee part of the class.
#'''January 26'''. Doing science: Falsifiability and Integrity.
#:''Assignment'': Summarize the essays ''Cargo Cult Science'' by Feynman, and ''Science: Conjectures and Refutations'' by Popper, and Ellis and Silk, 2014. I would expect you to identify 1-2 main points in each of the essays (at least three total), and list 1-2 questions about each essay (at least three total) that you would like to discuss. As always, if you found something surprising or hard to believe, or that you don’t agree with, please note that in your summaries. You should bring a copy of your summary to class to help you participate in discussions.
#'''January 28'''. How do we update our beliefs? Probability and Bayes theorem.
#:''Assignment'': Khan Academy lectures on ''Probability and Statistics'', pay particular attention to the Monty Hall problem/Bayes theorem. You may also want to read Feynman's lecture on ''Probability''. Summarize your understanding of the Bayes theorem. What would you like me to explain? As always, three points and three questions.
#:''Lecture'': I will give a lecture on basic probability theory and Bayes theorem, and how it is used to verify the laws of nature.
#'''February 2'''. How do we update our beliefs? Probability and Bayes theorem. Part II
#:''Assignment'': No new reading assignment. I suggest you read/listen the previous class assignment again, and see if you understand things now that you didn't understand before.
#:''Lecture'': I will give a lecture on basic probability theory and Bayes theorem, and how it is used to verify the laws of nature.
#'''February 4'''. How do we update our beliefs? Probability and Bayes theorem. Part III
#:''Assignment'': Wigner's essay on unreasonable effectiveness of math. Snow's essay on the asymmetry in math/science and humanities in the general culture. Please provide an itemized list of your own understanding of why "the book of nature is written in the language of mathematics" (this is a quote from Galileo).
#'''February 9''': Why math? and Matters arising: Do we use Bayesian inference in everyday life?
#:''Assignment'': Kording and Wolpert article on Bayesian integration.
#'''February 11''': The structure of scientific revolution
#:''Assignment'': Kuhn's book (or its wiki summary) on The structure of scientific revolution. In addition to the usual three points/three questions, think of a few examples of scientific revolutions and examples of continuous progress. Can you think of contradictions to Kuhn's ideas?
#'''February 16''':
#:Reading: papers for the upcoming seminar by de Polavieja. Read Perez-Escudero and de Polavijea, 2011.
#:''Assignment'': questions about the paper above.
#'''February 18''': Attending seminar: Gonzalo de Polavieja, http://www.quantitative.emory.edu/events/speakerseries1.html . Do
#: Do not come to the classroom, but go directly to the seminar room in the Modern Languages Building.
#: No written assignment.
#'''February 23''': Character of Physical Law, Lecture 1. Law of Gravitation.
#:''Assignment'': Summary and questions about the Lecture 1.
#:''Assignment'': Summary of the lecture by Gonzalo Polavieja; feel free to post questions if you have them as well, but this is not required.
#'''February 25''': Snow day, '''no class'''.
#'''March 2''' and '''March 4''' -- classes rescheduled, '''no classes'''.
#'''March 9''' and '''March 11''' -- spring break, '''no classes'''.
#'''March 16''': Character of Physical Law, Lecture 2. The Relation of Mathematics to Physics.
#:''Discussion Lead'': Alex Lin
#: Assignment: Summary and questions about the Lecture 2. '''Assignment Due''': March 2, 9:30 am.
#'''March 18''': Character of Physical Law, Lecture 3. The Great Conservation Principles.
#:''Discussion Lead'': Scott Weitzner
#: Assignment: Summary and questions about the Lecture 3. '''Assignment Due''': March 4, 9:30 am.
#'''March 20''', 11:30 am: Character of Physical Law, Lecture 4. Symmetry in Physical Law.
#:''Discussion Lead'': James Martin
#: Assignment: Summary and questions about the Lecture 4. '''Assignment Due''': March 16, 9:30 am.
#'''March 23''': Character of Physical Law, Lecture 5. The Distinction of Past and Future
#:''Discussion Lead'': Jonathan Kaminski
#: Assignment: Summary and questions about the Lecture 5. '''Assignment Due''': March 18, 9:30 am.
#'''March 24''', 8:45 am: Character of Physical Law, Lecture 6. Probability and Uncertainty.
#:''Discussion Lead'': Zheng Qiao
#: Assignment: Summary and questions about the Lecture 6. '''Assignment Due''': Mar 23, 9:30 am.
#'''March 25''': Character of Physical Law, Lecture 7. Seeking New Laws.
#:''Discussion Lead'': Dorcas Adedoja, '''Assignment Due''': Mar 25, 9:30 am
#: Assignment: Summary and questions about the Lecture 7.
#'''March 30'''
#:Reading: papers for the upcoming seminar by Murthy. Coen et al., 2014, ''Nature''.
#: Assignment: Summary and questions about the Coen et al. paper above.
#'''April 1'''
#; Attending seminar: Mala Murthy, http://www.quantitative.emory.edu/events/speakerseries1.html
#'''April 6''': How much detail is too much?
#: Assignment: Questions and summary of the following pieces: Rosenblueth and Wiener, L Carroll, JL Borges
#:''Discussion Lead'': Jin Rim
#'''April 8''': More is different! -- This is how new theories emerge
#: Assignment: Questions and summary of Weisskopf and Anderson articles. Compare and contrast their ideas.
#:''Discussion Lead'': Daniel Rodriguez
#'''April 13''': How do new theories emerge at longer scales?
#: Assignment: Questions and summary of the Wilson article.
#:''Discussion Lead'': Kyle Spitzer
#'''April 15''': How do we describe emergent theories?
#:Assignment: Questions and summary of Goldenfeld/Kadanoff article and Lazebnik article. Are they talking about the same thing? Why yes or why no?
#:''Discussion Lead'': Cherisse Wilkins
#'''April 20''': How do we find which laws of nature to discover?
#:Assignment: Questions and summary about Hamming's lecture.
#:''Discussion Lead'': TBA
#'''April 22'''. Project presentations.
#'''April 27'''. Project presentations.

==Reading==
In (roughly) chronological order. Notice that '''not all''' of these pieces will be assigned for you in class. Some are for your enjoyment only.
*L Carroll, [http://etc.usf.edu/lit2go/211/sylvie-and-bruno-concluded/4652/chapter-11-the-man-in-the-moon/ Sylvie and Bruno Concluded. Chapter 11: The Man in The Moon] (see passage about the pocket map), 1893.
*A Rosenblueth and N Wiener, The Role of Models in Science, ''Philosophy of Science'' '''12''':316, 1945. [[media:rosenblueth-wiener-1945.pdf|PDF]].
*JL Borges, [http://www.digiovanni.co.uk/borges/the-maker/of-exactitude-in-science.htm Of Exactitude in Science], translated by NT di Giovanni, 1946.
*K Popper, Science: Conjectures and Refutations, Lecture at Peterhouse, Cambridge, 1953. ''Removed due to copyright request''.
*CP Snow, ''The Two Cultures and The Scientific Revolution'', Cambridge UP, 1959. [[media:snow-1959.pdf|PDF]].
*EP Wigner, The Unreasonable Effectiveness of Mathematics in the Natural Sciences, ''Communications on Pure and Applied Mathematics'' '''13''':1, 1960. [[media:wigner-1960.pdf|PDF]].
*TS Kuhn, ''The Structure of Scientific Revolutions'', U Chicago Press, 1962. [[media:kuhn-1970.pdf|PDF]]. See also this [http://en.wikipedia.org/wiki/The_Structure_of_Scientific_Revolutions Wikipedia article].
*RP Feynman, [http://feynmanlectures.caltech.edu/I_03.html The Relation of Physics to Other Sciences], in ''The Feynman Lectures on Physics'', 1963.
*RP Feynman, [http://www.feynmanlectures.caltech.edu/I_06.html Probability], in ''The Feynman Lectures on Physics'', 1963.
*RP Feynman, [http://www.feynmanlectures.caltech.edu/I_12.html What is Force?], in ''The Feynman Lectures on Physics'', 1963.
*V Weisskopf, In Defence of High Energy Physics, ''Nature of Matter: Purposes of High Energy Physics'', 1965. [[media:weisskopf-1965.pdf|PDF]].
*RP Feynman, ''The Character of Physical Law'', Modern Library, New York, 1994. [[media:feynman-1965.pdf|PDF]]. Also available as annotated videos of Feynman's 1964 Messenger Lectures from Microsoft Research. Videos and the book are equivalent, you either need to read or to watch. I would watch the lectures -- there's magic in how Feynman delivers them, which gets lost in the transcribed version:
**http://research.microsoft.com/apps/tools/tuva/# -- Project Tuva. There are 7 lectures total, and we will study all of them.
*PW Anderson. More is different, ''Science'' '''177''':393, 1972. [[media:anderson-1972.pdf | PDF]].
*RP Feynman, [http://neurotheory.columbia.edu/~ken/cargo_cult.html Cargo Cult Science], 1974.
*KG Wilson, Problems in Physics with Many Scales of Length, ''Scientific American'' '''241''':140, 1979. [[media:wilson-1979.pdf|PDF]].
*RP Feynman, [https://www.youtube.com/watch?v=FXiOg5-l3fk The pleasure of finding things out], BBC/PBS Interview, 1981.
*R Hamming, You And Your Research, [http://www.cs.virginia.edu/~robins/YouAndYourResearch.html Bell Communications Research Colloquium Seminar], 1986.
*N Goldenfeld and LP Kadanoff, Simple lessons from complexity, ''Science'' '''284''':87, 1999. [[media:goldenfeld-kadanoff-1999.pdf|PDF]].
*Y Lazebnik, Can a Biologist Fix a Radio? —or, What I Learned while Studying Apoptosis. ''Biochemistry (Moscow)'' '''69'''(12):1403, 2002. [[media:lazebnik-2002.pdf|PDF]].
*K Kording and D Wolpert, Bayesian integration in sensorimotor learning. ''Nature'' '''427''':244, 2004. [[media:kording-wolpert-04.pdf|PDF]].
*F Wilczek, Whence the force of F= ma? I: Culture shock, ''Physics Today'' '''57'''(10):11, 2004. [[media:wilczek-04a.pdf|PDF]].
*F Wilczek, Whence the force of F= ma? II: Rationalizations, ''Physics Today'' '''57'''(12):10, 2004. [[media:wilczek-04b.pdf|PDF]].
*F Wilczek, Whence the force of F= ma? III: Cultural diversity, ''Physics Today'' '''58'''(7):10, 2005. [[media:wilczek-05.pdf|PDF]].
*D Deutsch, [https://www.youtube.com/watch?v=folTvNDL08A TED: A new way to explain explanation], 2009.
*A Pérez-Escudero and G de Polavieja G. Collective Animal Behavior from Bayesian Estimation and Probability Matching. ''PLoS Comput Biol'' '''7'''(11): e1002282, 2011. [[media:perez-escudero-11.pdf|PDF]].
*S Arganda, A Pérez-Escudero, and G de Polavieja, A common rule for decision making in animal collectives across species, ''PNAS'' '''109''':20508, 2012. [[media:arganda-12.pdf|PDF]].
*P Steinhardt, Big Bang blunder bursts the multiverse bubble, ''Nature'' '''510''':9, 2014. [[media:steinhardt-2014.pdf|PDF]].
*P Coen, J Clemens, A Weinstein, D Pacheco, Y Deng, and M Murthy. Dynamic sensory cues shape song structure in Drosophila, ''Nature'' '''507''':233, 2014. [[media:coen-etal-14.pdf|PDF]].
*G Ellis and J Silk, Scientific method: Defend the integrity of physics, ''Nature'' '''516''':321, 2014. [[media:ellis-silk-2014.pdf|PDF]].

And some additional reading for those who want to venture farther.
*Mathematical universe hypothesis: M Tegmark, [http://books.google.com/books/about/Our_Mathematical_Universe.html?id=MHufngEACAAJ Our Mathematical Universe: My Quest for the Ultimate Nature of Reality], Knopf, 2014.
**See also a critical review by [http://www.math.columbia.edu/~woit/wordpress/?p=6551 Peter Woit].
*S Wolfram, [http://books.google.com/books/about/New_Kind_of_Science.html?id=UvqpAAAACAAJ A new kind of science], Wolfram Media, 2002.
**See also critical reviews by [http://vserver1.cscs.lsa.umich.edu/~crshalizi/reviews/wolfram/ Cosma Shalizi], and [http://online.kitp.ucsb.edu/online/colloq/nemenman2/ myself].

And some encyclopedia articles:
*I Kant, [http://plato.stanford.edu/entries/kant-science/ Philosophy of Science] and [http://plato.stanford.edu/entries/kant-mathematics/ Philosophy of mathematics], in ''Stanford Encyclopedia of Philosophy''.
*[http://en.wikipedia.org/wiki/Scientific_theory Scientific theory] in ''Wikipedia''.
*[http://en.wikipedia.org/wiki/Physical_law Scientific law] in ''Wikipedia''.
*[http://plato.stanford.edu/entries/laws-of-nature/ Laws of nature] in ''Stanford Encyclopedia of Philosophy''.
*[http://en.wikipedia.org/wiki/Falsifiability Falsifiability] in ''Wikipedia''.
*[http://en.wikipedia.org/wiki/Not_even_wrong Not even wrong] in ''Wikipedia''.

Online classes:
*[https://www.khanacademy.org/math/probability/independent-dependent-probability/dependent_probability/v/introduction-to-dependent-probability Khan Academy Probability and Statistics] classes

File:TMLS ML.pdf

2020-05-11T16:11:55Z

Ilya: Flyer for the workshop

== Summary ==
Flyer for the workshop

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-23T16:38:58Z

Ilya: /* Lecture Notes and Detailed Schedule */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is unlikely to change a lot.
*[https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%206.%20Parallel%20Processing.ipynb Chapter 6], Parallel processing, this notebook is being actively edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.
*[https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2]. Submit Apr 13.
*[https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%205%2C%20Progress%20Report%201.ipynb Module 5, Progress Report 1]. Submit Apr 27.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:[https://emory.zoom.us/rec/share/-PQyAbztym9IG6uW5xneQvYNJtjAT6a81HBI-fAMzYfpELcYLd2rmxWm8nPQnRc Qihan's 04/16 Lab]
:[https://emory.zoom.us/rec/share/xPJWaLD-rVtIQbfqr03TV5FmGYXET6a8gClI-aYLmUeFvHZ4SjN-XKbR--Xn7AGg Emma's 04/17 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the ''Parallel processing'' notebook up to (not including) ''Newton's law of cooling''.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: ''Parallel processing'' notebook, introduction to spatially extended systems -- partial differential equations. Read until (including) ''Solving the Diffusion Equation using Python''
;Class 04/22: First attempts to do parallel processing, up to (not including) ''Diffusion on multiple processors''
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module), Submit Apr 27
;Class 04/27: wrap up, review for final. Quiz 5 due Apr 28 10am
;Recordings:
: [https://emory.zoom.us/rec/share/ypxxPa37r1xLG7eWuVuHdfY_H478T6a80SRIqaIMmNZYcXK-6OK-Qo8tx3PQ60Y Class 04/15]
: [https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's office hour 04/16]
: [https://emory.zoom.us/rec/share/puxsc5zM-UlJXK_My1D5BYECPZ-_eaa80yAWrvEPzR0hM7fGoCpxW0IE2XPi5ivi Qihan's office hour 04/19]
: [https://emory.zoom.us/rec/share/ysZePqDR_H1Ibc_Q4V-cQfB_FJzZaaa81igfqfVYz0YFmRFv_fZznYFwmH0iUSYP Class 04/20]
: [https://emory.zoom.us/rec/share/4eNWfqDb8m5Of7OUyF3lWrQ7Q6S0eaa81XAW_ftezRsqirEMoNThgZgdig8RUC_4 Class 04/22]
: If office hours are not posted, it means that nobody showed up, and there was no recording.

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-23T16:38:43Z

Ilya: /* Lecture Notes and Detailed Schedule */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is unlikely to change a lot.
*[https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%206.%20Parallel%20Processing.ipynb Chapter 6], Parallel processing, this notebook is being actively edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.
*
[https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2]. Submit Apr 13.
*
[https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%205%2C%20Progress%20Report%201.ipynb Module 5, Progress Report 1]. Submit Apr 27.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:[https://emory.zoom.us/rec/share/-PQyAbztym9IG6uW5xneQvYNJtjAT6a81HBI-fAMzYfpELcYLd2rmxWm8nPQnRc Qihan's 04/16 Lab]
:[https://emory.zoom.us/rec/share/xPJWaLD-rVtIQbfqr03TV5FmGYXET6a8gClI-aYLmUeFvHZ4SjN-XKbR--Xn7AGg Emma's 04/17 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the ''Parallel processing'' notebook up to (not including) ''Newton's law of cooling''.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: ''Parallel processing'' notebook, introduction to spatially extended systems -- partial differential equations. Read until (including) ''Solving the Diffusion Equation using Python''
;Class 04/22: First attempts to do parallel processing, up to (not including) ''Diffusion on multiple processors''
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module), Submit Apr 27
;Class 04/27: wrap up, review for final. Quiz 5 due Apr 28 10am
;Recordings:
: [https://emory.zoom.us/rec/share/ypxxPa37r1xLG7eWuVuHdfY_H478T6a80SRIqaIMmNZYcXK-6OK-Qo8tx3PQ60Y Class 04/15]
: [https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's office hour 04/16]
: [https://emory.zoom.us/rec/share/puxsc5zM-UlJXK_My1D5BYECPZ-_eaa80yAWrvEPzR0hM7fGoCpxW0IE2XPi5ivi Qihan's office hour 04/19]
: [https://emory.zoom.us/rec/share/ysZePqDR_H1Ibc_Q4V-cQfB_FJzZaaa81igfqfVYz0YFmRFv_fZznYFwmH0iUSYP Class 04/20]
: [https://emory.zoom.us/rec/share/4eNWfqDb8m5Of7OUyF3lWrQ7Q6S0eaa81XAW_ftezRsqirEMoNThgZgdig8RUC_4 Class 04/22]
: If office hours are not posted, it means that nobody showed up, and there was no recording.

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-23T16:35:10Z

Ilya: /* Module 5 */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:[https://emory.zoom.us/rec/share/-PQyAbztym9IG6uW5xneQvYNJtjAT6a81HBI-fAMzYfpELcYLd2rmxWm8nPQnRc Qihan's 04/16 Lab]
:[https://emory.zoom.us/rec/share/xPJWaLD-rVtIQbfqr03TV5FmGYXET6a8gClI-aYLmUeFvHZ4SjN-XKbR--Xn7AGg Emma's 04/17 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the ''Parallel processing'' notebook up to (not including) ''Newton's law of cooling''.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: ''Parallel processing'' notebook, introduction to spatially extended systems -- partial differential equations. Read until (including) ''Solving the Diffusion Equation using Python''
;Class 04/22: First attempts to do parallel processing, up to (not including) ''Diffusion on multiple processors''
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module), Submit Apr 27
;Class 04/27: wrap up, review for final. Quiz 5 due Apr 28 10am
;Recordings:
: [https://emory.zoom.us/rec/share/ypxxPa37r1xLG7eWuVuHdfY_H478T6a80SRIqaIMmNZYcXK-6OK-Qo8tx3PQ60Y Class 04/15]
: [https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's office hour 04/16]
: [https://emory.zoom.us/rec/share/puxsc5zM-UlJXK_My1D5BYECPZ-_eaa80yAWrvEPzR0hM7fGoCpxW0IE2XPi5ivi Qihan's office hour 04/19]
: [https://emory.zoom.us/rec/share/ysZePqDR_H1Ibc_Q4V-cQfB_FJzZaaa81igfqfVYz0YFmRFv_fZznYFwmH0iUSYP Class 04/20]
: [https://emory.zoom.us/rec/share/4eNWfqDb8m5Of7OUyF3lWrQ7Q6S0eaa81XAW_ftezRsqirEMoNThgZgdig8RUC_4 Class 04/22]
: If office hours are not posted, it means that nobody showed up, and there was no recording.

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-23T16:30:22Z

Ilya: /* Module 5 */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:[https://emory.zoom.us/rec/share/-PQyAbztym9IG6uW5xneQvYNJtjAT6a81HBI-fAMzYfpELcYLd2rmxWm8nPQnRc Qihan's 04/16 Lab]
:[https://emory.zoom.us/rec/share/xPJWaLD-rVtIQbfqr03TV5FmGYXET6a8gClI-aYLmUeFvHZ4SjN-XKbR--Xn7AGg Emma's 04/17 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the ''Parallel processing'' notebook up to (not including) ''Newton's law of cooling''.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: ''Parallel processing'' notebook, introduction to spatially extended systems -- partial differential equations. Read until (including) ''Solving the Diffusion Equation using Python''
;Class 04/22: First attempts to do parallel processing, up to (not including) ''Diffusion on multiple processors''
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module), Submit Apr 27
;Class 04/27: wrap up, review for final. Quiz 5 due Apr 28 10am
;Recordings:
: [https://emory.zoom.us/rec/share/ypxxPa37r1xLG7eWuVuHdfY_H478T6a80SRIqaIMmNZYcXK-6OK-Qo8tx3PQ60Y Class 04/15]
: If office hours are not posted, it means that nobody showed up, and there was no recording.

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-19T21:45:35Z

Ilya: /* Module 5 */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:[https://emory.zoom.us/rec/share/-PQyAbztym9IG6uW5xneQvYNJtjAT6a81HBI-fAMzYfpELcYLd2rmxWm8nPQnRc Qihan's 04/16 Lab]
:[https://emory.zoom.us/rec/share/xPJWaLD-rVtIQbfqr03TV5FmGYXET6a8gClI-aYLmUeFvHZ4SjN-XKbR--Xn7AGg Emma's 04/17 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the 'Parallel processing' notebook up to (not including) 'Newton's law of cooling' -- I will add more information to the notebook shortly. Also download 'diffusion_module.py' from the repository -- I will explain in class what it is for.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: 'Parallel processing' notebook, introduction to spatially extended systems -- partial differential equations. Read until (including) 'Solving the Diffusion Equation using Python'
;Class 04/22: More work on parallel processing
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module), Submit Apr 27
;Class 04/27: wrap up, review for final. Quiz 5 due Apr 28 10am
;Recordings:
: [https://emory.zoom.us/rec/share/ypxxPa37r1xLG7eWuVuHdfY_H478T6a80SRIqaIMmNZYcXK-6OK-Qo8tx3PQ60Y Class 04/15]
: If office hours are not posted, it means that nobody showed up, and there was no recording.

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-19T21:45:04Z

Ilya: /* Module 5 */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:[https://emory.zoom.us/rec/share/-PQyAbztym9IG6uW5xneQvYNJtjAT6a81HBI-fAMzYfpELcYLd2rmxWm8nPQnRc Qihan's 04/16 Lab]
:[https://emory.zoom.us/rec/share/xPJWaLD-rVtIQbfqr03TV5FmGYXET6a8gClI-aYLmUeFvHZ4SjN-XKbR--Xn7AGg Emma's 04/17 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the 'Parallel processing' notebook up to (not including) 'Newton's law of cooling' -- I will add more information to the notebook shortly. Also download 'diffusion_module.py' from the repository -- I will explain in class what it is for.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: 'Parallel processing' notebook, introduction to spatially extended systems -- partial differential equations. Read until (including) 'Solving the Diffusion Equation using Python'
;Class 04/22: More work on parallel processing
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module), Submit Apr 27
;Class 04/27: wrap up, review for final. Quiz 5 due Apr 28 10am
;Recordings:
:[https://emory.zoom.us/rec/share/ypxxPa37r1xLG7eWuVuHdfY_H478T6a80SRIqaIMmNZYcXK-6OK-Qo8tx3PQ60Y Apr 15 lecture]

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-19T21:30:12Z

Ilya: /* Module 5 */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:[https://emory.zoom.us/rec/share/-PQyAbztym9IG6uW5xneQvYNJtjAT6a81HBI-fAMzYfpELcYLd2rmxWm8nPQnRc Qihan's 04/16 Lab]
:[https://emory.zoom.us/rec/share/xPJWaLD-rVtIQbfqr03TV5FmGYXET6a8gClI-aYLmUeFvHZ4SjN-XKbR--Xn7AGg Emma's 04/17 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the 'Parallel processing' notebook up to (not including) 'Newton's law of cooling' -- I will add more information to the notebook shortly. Also download 'diffusion_module.py' from the repository -- I will explain in class what it is for.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: 'Parallel processing' notebook, introduction to spatially extended systems -- partial differential equations. Read until (including) 'Solving the Diffusion Equation using Python'
;Class 04/22: More work on parallel processing
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module), Submit Apr 27
;Class 04/27: wrap up, review for final. Quiz 5 due Apr 28 10am

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-18T17:03:35Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:[https://emory.zoom.us/rec/share/-PQyAbztym9IG6uW5xneQvYNJtjAT6a81HBI-fAMzYfpELcYLd2rmxWm8nPQnRc Qihan's 04/16 Lab]
:[https://emory.zoom.us/rec/share/xPJWaLD-rVtIQbfqr03TV5FmGYXET6a8gClI-aYLmUeFvHZ4SjN-XKbR--Xn7AGg Emma's 04/17 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the 'Parallel processing' notebook up to (not including) 'Newton's law of cooling' -- I will add more information to the notebook shortly. Also download 'diffusion_module.py' from the repository -- I will explain in class what it is for.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: 'Parallel processing' notebook, introduction to spatially extended systems -- partial differential equations, introduction to parallel processing
;Class 04/22: More work on parallel processing
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module), Submit Apr 27
;Class 04/27: wrap up, review for final. Quiz 5 due Apr 28 10am

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-18T16:17:42Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:[https://emory.zoom.us/rec/share/xPJWaLD-rVtIQbfqr03TV5FmGYXET6a8gClI-aYLmUeFvHZ4SjN-XKbR--Xn7AGg Emma's 04/17 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the 'Parallel processing' notebook up to (not including) 'Newton's law of cooling' -- I will add more information to the notebook shortly. Also download 'diffusion_module.py' from the repository -- I will explain in class what it is for.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: 'Parallel processing' notebook, introduction to spatially extended systems -- partial differential equations, introduction to parallel processing
;Class 04/22: More work on parallel processing
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module), Submit Apr 27
;Class 04/27: wrap up, review for final. Quiz 5 due Apr 28 10am

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-16T20:27:24Z

Ilya: /* Module 5 */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the 'Parallel processing' notebook up to (not including) 'Newton's law of cooling' -- I will add more information to the notebook shortly. Also download 'diffusion_module.py' from the repository -- I will explain in class what it is for.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: 'Parallel processing' notebook, introduction to spatially extended systems -- partial differential equations, introduction to parallel processing
;Class 04/22: More work on parallel processing
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module), Submit Apr 27
;Class 04/27: wrap up, review for final. Quiz 5 due Apr 28 10am

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-16T19:41:32Z

Ilya: /* Module 5 */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the 'Parallel processing' notebook up to (not including) 'Newton's law of cooling' -- I will add more information to the notebook shortly. Also download 'diffusion_module.py' from the repository -- I will explain in class what it is for.
;Labs 04/16-04/17: Work on projects for Module 4 -- Stochastic Simulations, and submit your report on Monday April 20
;Class 04/20: 'Parallel processing' notebook, introduction to spatially extended systems -- partial differential equations, introduction to parallel processing
;Class 04/22: More work on parallel processing
;Labs 04/23-04/24: Module 5, Progress report 1 (No final project for this module)

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-14T23:04:08Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:[https://emory.zoom.us/rec/share/x_coMuDa23NLHbfp6nzUQpwMWaLfaaa81ygZ-fAEykggk_fuFN_maOkj71bKUuHS?startTime=1586786214000 Class 04/13]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the 'Stochastic simulations' notebook up to (not including) 'Newton's law of cooling' -- I will add more information to the notebook shortly. Also download 'diffusion_module.py' from the repository -- I will explain in class what it is for.

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-14T23:00:44Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/wPx3C5Ws6GJOYIHs9mDiQ7ImR6jDX6a80yFI-PAKy0sPn92fcwlTjU7qsZ3p-kof Qihan's 04/09 Lab]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the 'Stochastic simulations' notebook up to (not including) 'Newton's law of cooling' -- I will add more information to the notebook shortly. Also download 'diffusion_module.py' from the repository -- I will explain in class what it is for.

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-14T23:00:00Z

Ilya: /* Module 5 */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===
;Class 04/15: Start reading the 'Stochastic simulations' notebook up to (not including) 'Newton's law of cooling' -- I will add more information to the notebook shortly. Also download 'diffusion_module.py' from the repository -- I will explain in class what it is for.

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-14T22:57:04Z

Ilya: /* Module 4 */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-12T17:20:15Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:[https://emory.zoom.us/rec/share/zvBMMpf0xmdLSaPN1hHeZIkNIab4X6a8gHRI_qIMzU6raVt5mf0iJXt5h7bj03Q8 Emma's 04/10 Office Hour]
:[https://emory.zoom.us/rec/share/ztBrCpf5zn9Ifa_G7GHmc6ksEN7rT6a8gyEX_PpenxunVah-AI7SwgQopBFOORp- Emma's 04/10 Lab]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-12T17:09:49Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Class 04/13: Read the 'Stochastic simulations' notebook, 'Projects' section, and understand the projects. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-09T15:21:13Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]
:[https://emory.zoom.us/rec/share/7JFzderh1kRLa53_xl3gB_4uFb71aaa8gSJI-PQImBpwukz_iUM_LTE7nhJruxgx Lab 04/03]
:[https://emory.zoom.us/rec/share/6_ZvEpvhxH5OXq-cuB3SUPd6LoXdX6a81CZPqftcyR3s5JISvsSXmI6TL0MJuR47 Class 04/06]
:[https://emory.zoom.us/rec/share/tO1IAprWrFhJH9bt1mrQCqkCBZ_feaa81SgX8qVZyxlMpmszxHiv82jtWPZHHDpG Class 04/08]
:If office hours are not posted, it means that nobody showed up, and there was no recording.

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-09T15:07:38Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Labs 11, Apr 9-10
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%202.ipynb Module 4, Progress Report 2] notebook. Submit it by Apr 13.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-07T22:34:38Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Class 04/08: Read the 'Stochastic simulations' notebook up to and including 'Central Limit Theorem' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-06T01:44:44Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]
:[https://emory.zoom.us/rec/share/7PRENu7W7nhIHo3nq1_8VIh4Lpr9T6a8hykdqadbyhqCmFR-R1c6cq0jki9-20Ev Lab 04/02]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-06T01:42:32Z

Ilya: /* Lecture Notes and Detailed Schedule */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1]. You were submitting the report without the notebook; it wasn't available at the time.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-06T01:41:56Z

Ilya: /* Lecture Notes and Detailed Schedule */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%202%2C%20Progress%20Report%201.ipynb Module 2, Progress Report 1].
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2]. Submit Mar 30
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%204%2C%20Progress%20Report%201.ipynb Module 4, Progress Report 1]. Submit Apr 6.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-06T01:39:18Z

Ilya: /* Lecture Notes and Detailed Schedule */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%205.%20Stochastic%20Simulations.ipynb Chapter 5], Stochastic simulations, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-06T01:21:31Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]
:[https://emory.zoom.us/rec/share/4OVXHu_VzVJLQKPz0WzHc_EtNKX0T6a82igcr_oEnU6RPKA11Wb8olhMmbKcqyTV Qihan's office hour]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-06T01:19:16Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]
:[https://emory.zoom.us/rec/share/xfwvMezN7URIYbPr6Eb9C_cjN9rBaaa8higWqaBczMi4O-mUuot9cxgk3c11piI Class 04/01]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-06T01:18:05Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]
:[https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT office hour 03/30]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-06T01:03:48Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Class 04/06: Read the 'Stochastic simulations' notebook up to and including 'What is the error of MC methods?' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-04-02T11:31:52Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Labs 10, Apr 2-3
: Do all exercises in the Module 4, Progress Report 1 notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Apr 6.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-31T18:03:32Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Class 04/01: Read the 'Stochastic simulations' notebook up to and including 'Exponential Random Numbers' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-30T22:30:11Z

Ilya: /* Module 3: Optimization */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]
: [https://emory.zoom.us/rec/share/1_R6H-7y2GNIWa_28Uz6YJYtOb3pT6a80yQY86Bez0vJ6Z5vVpt5oyBQt6qbWjsT Office hour 03/30]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-30T22:29:33Z

Ilya: /* Module 4: Stochastic simulations */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.
;Recordings
:[https://emory.zoom.us/rec/share/6_5FNZHK62JISYHI-lzPZ7AtNbjceaa80yRI_KEEyUtVO46NLqj86l7vuj48sIlo Class 03/30]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-29T18:43:38Z

Ilya: /* Module 3: Optimization */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.
*Class will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/117775655
*Office hours will meet virtually at the usual time at the following Zoom link https://emory.zoom.us/j/354960837

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Labs 8, Mar 5-6
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%202.ipynb Module 3, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by Mar 23 (date changed due to transition to virtual learning).
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Class 03/25: No pre-class questionnaire. Read notebooks and prepare for midterm. Come with questions that you think will help you during the exam.]
;Labs 9, Mar 26-27, virtual
: Work on the final projects for Module 3.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]
: [https://emory.zoom.us/rec/share/5uZkF77P3yRIaKvV2E6HR606MoHIT6a8gSIbq_VezEdJ2dk8WSmXsokp1Fe8tXnG Class 03/23]
: [https://emory.zoom.us/rec/share/-vxWH5zP6VpLZZHg133ZSIc7JrTmeaa803NK-fQEz0aHObs9MIPf-iW3jQtSEXrf Office hour 03/23]
: [https://emory.zoom.us/rec/share/9MBaE5uozD5LZJHG7B7PVPM4BKPJeaa8gXQZ-_UMxE89BjYJlaKdu5AHM1OURzjR Class 03/25]
: [https://emory.zoom.us/rec/play/uJB7JOyt-m43H4eVsQSDBPN4W9Xseqqs0yZN-_sKzxvmAnQDZlSuNOcUMLYS09NVpSnJOnKBeBow-rid?continueMode=true&_x_zm_rtaid=syMDeQ7KS3-CvJvysEvNIw.1585507078959.3a287e81dc6c0c0ff1ac3b19db7c61a8&_x_zm_rhtaid=630 Emma's 3/27 office hour]
: [https://emory.zoom.us/rec/share/5PMlJI-sqmxITYnT9mLQSvUmJNX1X6a8hHMa-_MIxE66vqwLCCuCmaojCE-0uZif Emma's 3/27 lab]
: [https://emory.zoom.us/rec/play/vpUoJuGvpz43G9OWuASDVqUsW9S9LK6s2ykcq6UKyBy2ByRQOlvyZuMaZOq9i9O-Wjo3z8Sa3vUJ1O_q?continueMode=true&_x_zm_rtaid=j42h_PZnQyqtSUUBBj-rhw.1585412206604.9561bb0b6bfa526cc4bdfebeb57b9a8d&_x_zm_rhtaid=675 Qihan's 3/26 lab]

===Module 4: Stochastic simulations===
;Class 03/30: Read the 'Stochastic simulations' notebook up to and including 'Random Numbers in Python' section. Do the appropriate questionnaire.

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-29T18:42:38Z

Ilya: /* Module 3: Optimization */

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-29T18:30:49Z

Ilya: /* Module 3: Optimization */

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-26T16:12:22Z

Ilya: /* Module 3: Optimization */

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-26T16:11:42Z

Ilya: /* Module 3: Optimization */

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-26T16:10:46Z

Ilya: /* Module 3: Optimization */

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-25T18:29:50Z

Ilya: /* Module 3: Optimization */

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-25T13:40:36Z

Ilya: /* Module 3: Optimization */

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-25T13:37:51Z

Ilya: /* Module 3: Optimization */

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-23T13:21:34Z

Ilya: /* News */

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-23T13:17:32Z

Ilya:

Physics 212, 2020: Syllabus

2020-03-22T13:52:14Z

Ilya: /* COVID-19 related changes */

{{PHYS212-2020}}

;Course Title: Computational Modeling for Scientists and Engineers
;Course Numbers: Physics 212/Biology 212
;Time/Place: M, W 10-11:15, MSC N304
;Lab: Th or F 2:30-5:30; MSC N303
;Professor: Ilya Nemenman ilya.nemenman@emory.edu (best way to contact me)
;TA: Qihan Liu (Thursday lab)
;TA: Emma Dawson (Friday lab)
;Office Hours
:Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00, MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, MSC N209
;Class Web Page: http://nemenmanlab.org/~ilya/index.php/Physics_212,_2020:_Computational_Modeling_For_Scientists_And_Engineers

==Communications==
The best way to contact me (questions about projects, notes about missing classes, scheduling a meeting -- literally, anything) is via email. I have multiple offices on campus, and it is unlikely that you will find me by simply dropping in outside of a regular office hour, unless we scheduled a meeting ahead of time. So please send me emails.

I receive a lot of email, and I employ automated sorting of my Inbox. If you want your message to be read, the subject of the email ''must'' start with '''PHYS/BIOL212'''. I will be responding to emails related to the class once a day, but not on weekends and holidays. I will be responding more often before major deadlines related to the class. Thus please do not expect a response instantaneously -- plan ahead, and ask questions early. Similarly, if you request a meeting with me in the last minute, I will likely not be available. You need to communicate with me at least a day or two ahead of time if you want to schedule a meeting. Beyond this, I strive to be as responsive as I can be, and to spend as much time as possible with every student who has questions. Please, respect my time: be on time, respond promptly, read emails before sending questions, and I will similarly respect your time.

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive problem of a natural phenomenon into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

===Textbooks===
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling'', http://press.princeton.edu/titles/10644.html
::This tutorial is not a complete textbook. I will try to post additional lecture notes online as needed, or to direct you to additional chapters in other textbooks.
:: See also [http://www.wiley.com/WileyCDA/WileyTitle/productCd-EHEP003413.html Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.

===Required Software===
*[https://www.anaconda.com/download/ Anaconda Python distribution]
*Install Python v 3.X (any minor release v. 3)
Note that coming to class (starting class 2) without a working Python distribution or without a laptop will result in a failing class participation grade.

===Pre-requisites===
Pre-requisites: two semesters of calculus and PHYS 151, or instructor consent. I do not require prior computing experience.

This class differs from most other classes in that we will use mathematical modeling and computer simulations as a language that glues students from very diverse backgrounds. Thus we will be spending many of our class hours ''programming in Python in class''. It is thus essential to have a laptop access ''in class'' and ''for homework". You will be working in groups of 3-4 students, depending on the eventual class enrollment (up to 10 groups in the class), and everyone is required to have laptops and a working Anaconda distribution.

===Class structure===
I request a lot from my students, but also provide them with all the necessary resources to succeed in the class. As a result, students will work hard, but will likely learn more than in a typical class. In practice, this philosophy is implemented as follows.

;Modules: The class will consists of modules of a few weeks long. Typically, each module will consist of traditional in-class lectures or tutorials, where the necessary concepts will be introduced (though we might deviate from this as needed). These will be interspersed with short coding exercises, which you will submit through a provided portal in-class; presence of these will be graded. These are designed to help you grasp the concepts studied in class and to get your feet wet with Python programming. The TAs and the professor will help you in these exercises.

;Labs: A core component of the class are the labs, conducted by the TAs, where you will be solving larger coding/modeling problems, eventually culminating in the final projects for each module, as well as gaining even more experience with Python. The lab problems will start simple, but will become more complex towards the end of the class.

;Quizzes: The last class period of each module will end with a 20-30 min quiz, which will test your comprehension of the material in the module. Barring extraordinary circumstances discussed with me ahead of the quiz class, there will be no makeup quizzes. One worst (or missing) quiz grade will be dropped.

;Reports: You will need to submit reports on projects for each module for grading, multiple times as you are developing these reports over the duration of the module. All the work that you do for in-class coding problems, lab coding projects, and final module projects will need to be completed by you at home, and then submitted for grading. The reports will need to be done using ''Jupyter Notebooks'', and you will submit the notebooks to me via Canvas. Don't worry if you do not know what Jupyter notebook is; we will study this in class. While you can do the programming collectively with other students (I encourage this, in fact), your submissions will be individual. Submissions are due by '''9 am on Monday''' every week (unless Monday is a holiday), starting the first week of class. I will accept '''one late submission''' (up to 48 hours) per student over the course of the semester; you do not need to notify me of a submission delay for this one time. Submissions late by more than 48 hours, or more than one late submission will not be graded and '''will receive a grade of zero''', unless an extension has been requested and granted not later than Friday before the deadline, or there is a documented last-minute emergency.

:The notebooks you submit -- even if they are just progress reports -- must not be rough drafts. Each cell must be executable with no errors, and you must document your code. The notebooks should start with
:#Header: your name, module number, names of other group members.
:For each of the final module reports, Jupyter notebook report should contain the following sections. Each section can be one or multiple cells.
:#Name of the specific project you chose.
:#Short analysis of the problem: Using Scientific American level language, provide a short (few sentences) description of the problem you are solving. Focus on objectives of the study, on what the result of your simulations / analysis will be.
:#Model design: Explain in one paragraph or so how you translate a problem into a computational model. Explain your assumptions and why you made them. Define every symbol you use. Use figures (import them into Jupyter) to illustrate the model and label the diagram of relations among variables.
:#Model solution: This will be the Python code solving the problem per se. Note that the code must be documented -- annotations must explain the general logic of the code, and what specific functions and language constructs do.
:#Results, verification, and conclusion or discussion: Include results (typically numerical values or graphs; importantly, all figures should have titles, axes labels, legends, etc.) of your solution. Explain how you have convinced yourself that the results are valid (that is, how you verified the code). Interpret and explain your results. Explain what, if anything, should have been done differently.

;Partitioning into groups: There will be 5 modules in the class. I expect you to work in groups of 3-4 on each module. You must not be in the same group with any other student more than twice over the course of the semester. Beyond this, please subdivide in your working groups on your own. Notice that no group should be larger than 4 people, but they may be smaller. In fact, you may work on your own if you'd like -- though I don't encourage this.

;Homework: Besides coding problems, discussed above in the ''Reports'' section, there will be no other graded homework sets. However, preparing the reports will require substantial work at home / in the lab.

;Office hours: I will have regular office hours every week. So will the TA (at a different time). In addition, we will have review sessions before the exams, or when it becomes clear that many of you have similar concerns that must be addressed.

;Exams: We will have one '''midterm''' and '''the final exam''' in addition to the quizzes. During these exams, you will be required to answer questions about the concepts we studied in class, as well as to sketch pseudocode or write Python code solving smaller modeling problems. Having a laptop is mandatory during exams. '''Final exam: May 5, 8 am'''

;Laptops: Having a laptop with a working Anaconda installation is mandatory starting the second class.

;Special note: I will need to travel professionally during the semester. As a result, a few classes will be conducted by guest lecturers and/or the TAs. As of the beginning of the semester, I will be away on Feb 19, Mar 4 and possibly Apr 8. I will update the dates of classes that will be taught by guests as I get more informations.

;Updates: Updates will be posted in the News section of the class web site and emailed to the enrolled students through Canvas. It's your responsibility to check your email and the News section the night before each class.

;Weather closures: For ''Short-term University Closures'' (defined as one or two days), changes will be made to the course syllabus to cover the appropriate content during regular class sessions upon return from closure. For "Long-term University Closures" (defined as three or more days), the College has reserved all Registrar scheduled classrooms over the course of two weekends to allow for in-person class meetings to account for the time missed. I will announce these make-up days as needed.

===Grading===
*Lab participation / attendance -- 5%.
**You need to be present at 11 labs (80% of 14 labs) to get the full grade. Please don't inundate the TAs with notes from coaches, doctors, etc. It is your responsibility to make sure that your attendance is recorded by the TA.
*Quizzes -- 15% (cumulative for all modules, one worst/missing quiz grade will be '''dropped''').
*Reports -- 45% (cumulative for all modules, one worst/missing report grade will be '''dropped''' for the final report and cumulative progress). Of these, 25% will be the grades you get for the final reports for each module, and 20% of the grade will be accumulated for the weekly progress sumbissions.
*Midterm -- 15%.
*Final exam -- 20%.

Your scores will convert to a letter grade as follows:
*93.0 - 100 A
*90.0 – 92.9 A-
*87.0 – 89.9 B+
*83.0 – 86.9 B
*80.0 – 82.9 B-
with the pattern repeating for C and D grades; 59.9 or less is a failing grade.

===Honor code===
The Emory College Honor Code applies to all homework assignments.

===Tentative class schedule===
The schedule of topics covered during each lecture is subject to change. I may need to revise it to reflect the pace of the class. The current schedule can be found on the class web site.
Labs start on Jan 16

;Module 1: Introduction to modeling process, Python programming language, Spyder, Jupyter Notebooks, simple plotting. Review of some calculus concepts. Projects Topic: solving an algebraic equation.
::Jan 15, 22, 27, 29, Feb 3
::Feb 3: Quiz 1
::''Progress Report: Jan 27, Feb 3''
::''Final Report: Feb 10''
;Module 2: Modeling dynamics of systems described by multiple variables, computational errors, simulation techniques for deterministic dynamics, Python functions, modules, and scopes, advanced plotting. Project Topics: solving systems of coupled differential equations describing various natural phenomena.
::Feb 5, 10, 12, 17, 19
::Feb 19: Quiz 2
::''Progress Report: Feb 17''
::''Final Report: Feb 24''
;Module 3: Data Driven Models -- Fitting Models to Data: Linear regression and other empirical models, optimization and optimization methods, curve fitting. Project Topics: fitting nonlinear curves to experimental data.
::Feb 24, 26, Mar 2, 4, 16
::''Mar 9, 11: Spring break, no classes''
::Mar 16: Quiz 3
::''Progress Reports: Mar 2, 16''
::''Final Report: Mar 23''
;Mar 18 -- Midterm
;Module 4: Simulations with Randomness, random numbers and random walks, cellular automata and agent-based models. Project Topics: pattern formation in stochastic systems.
::Mar 25, 30, Apr 1, 6, 8
::Apr 8: Quiz 4
::''Progress Reports: Mar 30, Apr 6''
::''FInal Report: Apr 13''
;Module 5: High Performance Computing. Project topics: solving partial differential equations on multiple cores.
::Apr 13, 15, 20, 22
::Apr 27: Quiz 5
::''Progress Reports: Apr 20''
::''Final Report: Apr 27''
;Apr 27 -- catch-up class; exam review.
;'''May 5, 8:00 am -- Final Exam'''

===Statement from the Department of Physics===
Please treat your classmates with respect both in and out of the classroom. It is unacceptable to discriminate against your fellow students on the basis of race, gender, perceived physics acumen, or any other reason. If you have any concerns, please let me know or contact the department chair, Prof. Stefan Boettcher.

===COVID-19 related changes===

;Summary: the course will run largely in an asynchronous manner, save for lectures and labs that will turn into large discussion sessions and working-together sessions. You will need to do work reading for lectures before they start.

;Lectures: I will make an effort of having my lecture notes at least 24 hours ahead of our regularly scheduled class times (MW, 10am EDT), posted on the course web site. I will not be recording video lectures, as these will be largely redundant with my lecture notes. For every lecture, I will post a questionnaire, which you will need to answer after reading the lecture materials, and at least an hour before the class time. I will use your answers to see which parts of the lecture are less clear for you, and adjust my teaching plan accordingly.

;Class sessions: (MW, 10am-11:15am EDT) These will be flipped — in the sense that I will not be delivering lectures, but only responding to your questions that emerge from pre-lecture questionnaires, and during the lectures. I expect you to attend these lectures, and have video on (I tried to work with video off, but it’s hard without getting the facial expression feedback), however, I will not be grading on attendance — especially because many of you are now scattered over various time zones across the world. Thus, to get the most out of these sessions, you should come prepared — having read the material, and having formulated questions. Class sessions will be recorded and posted on the course web site. The College has asked me to add the following information to the syllabus:

:::Lectures and other classroom presentations presented through video conferencing and other materials posted on Canvas are for the sole purpose of educating the students enrolled in the course. The release of such information (including but not limited to directly sharing, screen capturing, or recording content) is strictly prohibited, unless the instructor states otherwise. Doing so without the permission of the instructor will be considered an Honor Code violation, and may also be a violation of state or federal law, such as the Copyright Act. All University policies remain in effect for students participating in remote education.

;Quizzes and Midterm: These will be asynchronous, not in class time. The due dates for Quiz 3 will be March 24 at 10am (the quiz will open on Sunday night, and you will have 30 minutes to do it on your own time). The due date for the Midterm will be March 26 at 10am (the midterm will open on Tuesday, and you will have 2 hours between when you download it and when you submit the result). I will communicate the deadlines for other quizzes later.

;Final: Final will be asynchronous, you will be taking it on your own time. I don’t know when yet, and am waiting for instructions from the College.

;Labs: The TAs will let you know their specific instructions for the labs. Generally, the labs will be big discussion sessions, where you work in groups, in breakout rooms, on the code in the lab notebooks. Lab participation will not be graded from now on — the entire lab participation grade will be based on the first half of the semester.

;Grading: All of the grading policies remain the same except that the 5% lab participation grade will be split into: 2.5% for lab participation through the spring break and 2.5% for answering pre-lecture questionnaires for after the spring break. We had 7 labs before the break, and so you get full 2.5% for lab attendance if you attended 80% of those -- 5 out of 7 labs.

;Schedule: The semester is not being extended. This means that we lost two lecture classes over the course of the break. I do not know yet how we will catch up with those, and whether we will. Let’s see how the first week shapes up, and I will let you know later.

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-21T20:31:42Z

Ilya: /* Module 3: Optimization */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Jan Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Class 03/23: Finish reading the ''Optimization'' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Computational Modeling For Scientists And Engineers

2020-03-21T20:31:27Z

Ilya: /* Module 3: Optimization */

{{PHYS212-2020}}

==News==
*Welcome to the class!
*New sections are being added to the syllabus to account for the virtual learning we are switching to due to COVID-19.

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive formulation of a scientific problem into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

==Logistics==
*Class Hours: M, W 10:00-11:15; MSC N 304
*Labs: Thu or Fri 2:30-5:30; MSC N303
*Office Hours
:Professor: Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00 , MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, N209
*[[Physics 212, 2020: Syllabus|Syllabus]] -- I will try to keep close to the syllabus in the course of the semester, but some deviations are possible.
*[https://www.anaconda.com/download/ Anaconda Python distribution] (install Python v 3.X)
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling, 2nd edition'', http://press.princeton.edu/titles/10644.html . This is '''the only textbook you should have'''; all others are optional.
::This tutorial is not a complete textbook. I will post additional lecture notes online as needed, or will direct you to additional chapters in other textbooks.
:: See also [https://www.wiley.com/en-us/Computational+Modeling+and+Visualization+of+Physical+Systems+with+Python-p-9781119239888 Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.
*At the end of each class where we do coding, please '''submit your work''' using a ''Coding Snippet'' assignment submission on Canvas.

==Lecture Notes and Detailed Schedule==
*Class schedule is available in [[Physics 212, 2020: Syllabus|the syllabus]].
*Below I will post Python notebooks for this class. I will strive to post changes to these notebooks before classes, but no promises.
*The Notebooks will also have project assignments for you to work on.

All of the notebooks we will use in the class are available from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Currently the following notebooks are available:
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1], Introduction to Computational Modeling; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2], Learning Python and solving algebraic equations; this is finalized, and is unlikely to change a lot.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3], Building and Solving Dynamical Models, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4], Optimization, this notebook is still being edited.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook, which covers the Introduction, and Chapters 1 and 2 of the ''Student Guide''; this notebook is now finalized. You will need to (re)-submit this notebook on Jan 27th.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook, which covers Module 1 (Algebraic equations), and Chapters 3 and part of 4 of the ''Student Guide''. The notebook is now finalized, and you need to submit it on Feb 3.
* Module 2, Progress Report 1, notebook, is not available; just do Your Turn exercises from the Module 2 notebook, up to RK2 algorithm.
* [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook, which covers Module 3 up to and including the nonlinear 1-d optimization lecture (02/26). Submit this notebook on March 2.

===Introduction===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%201.%20Introduction.ipynb Chapter 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 1, Jan 16-17
: Instal Anaconda.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class, and exercises from Chapter 1 and Chapter 2 of the ''Student Guide''. Finalized version of this notebook would need to be submitted on Jan 27.
:;Reading: Chapters 1 and 2 and Appendix B of the Python Student Guide.

===Module 1: Learning Python and solving algebraic equations===
Download or view the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%202.%20Learning%20Python%20and%20solving%20algebraic%20equations.ipynb Chapter 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 2, Jan 23-24
: Do all exercises in the updated version of the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%201.ipynb Module 1, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit or re-submit this updated and complete notebook on Jan 27.
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 of the ''Student Guide''. Do not submit this notebook on Jan 27th, and updated version will be due Feb 3.
:;Reading: Chapters 3 of the Python Student Guide.
;Labs 3, Jan 30-31
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%201%2C%20Progress%20Report%202.ipynb Module 1, Progress Report 2] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. This includes Your Turn questions from class to date, and exercises from Chapter 3 and some of Chapter 4 of the ''Student Guide''. Submit the progress report by Feb 3.
:;Reading: Sections 4.1 and 4.2 and Appendix E of the Python Student Guide.
;Labs 4, Jan Feb 6-7
: Do the project for Module 1 and submit on Monday.

===Module 2: Dynamical models: Building and solving dynamical models===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%203.%20Building%20and%20Solving%20Dynamical%20Models.ipynb Chapter 3] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 5, Feb 13-14
:Do the 'Your Turn' exercises in the notebook up to (not including) RK2 and submit on Feb 17.
:;Reading: See reading assignment in the Chapter 3 notebook above.
;Labs 6, Jan Feb 20-21
: You are not required to do the new Your Turn questions (3.8 - 3.18); these won't be submitted since we have only one Progress Report for this module, not two. However, I strongly recommend that you try to do some of them in your spare time.
: Do the project for Module 2 and submit on Monday 2/24.

===Module 3: Optimization===
Download and read [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Chapter%204.%20Optimization.ipynb Chapter 4] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. ''Make sure to keep re-downloading the notebook, as I will change it in the course of the class.
;Labs 7, Jan Feb 27-28
: Do all exercises in the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook/blob/master/Module%203%2C%20Progress%20Report%201.ipynb Module 3, Progress Report 1] notebook from the [https://github.com/EmoryUniversityTheoreticalBiophysics/ComputationalModelingTextbook Lecture Textbook repository]. Submit the progress report by March 2.
;Class 03/23: Finish reading the 'Optimization' notebook (including the projects), respond to the questionnaire, and start thinking about the projects.
;Recordings:
: [https://emory.zoom.us/rec/play/u5Iof7_8_Tw3H9aSsASDA6N8W9Tve_-s13Ue-qAPnU28AXMFZFSnYrFAZbHFoQYAeRhHlWxXGsByfRjW Office hour 03/20 ]

===Module 4===

===Module 5===

[[Category:Ilya's Teaching]]

Physics 212, 2020: Syllabus

2020-03-20T21:31:24Z

Ilya: /* COVID-19 related changes */

{{PHYS212-2020}}

;Course Title: Computational Modeling for Scientists and Engineers
;Course Numbers: Physics 212/Biology 212
;Time/Place: M, W 10-11:15, MSC N304
;Lab: Th or F 2:30-5:30; MSC N303
;Professor: Ilya Nemenman ilya.nemenman@emory.edu (best way to contact me)
;TA: Qihan Liu (Thursday lab)
;TA: Emma Dawson (Friday lab)
;Office Hours
:Ilya Nemenman -- Monday and Thursday 12:00-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
:TA: Qihan Liu (Thursday lab), Office hour Monday 1:00-2:00, MSC N117E
:TA: Emma Dawson (Friday lab), Office hour Wednesday 2:30-3:30, MSC N209
;Class Web Page: http://nemenmanlab.org/~ilya/index.php/Physics_212,_2020:_Computational_Modeling_For_Scientists_And_Engineers

==Communications==
The best way to contact me (questions about projects, notes about missing classes, scheduling a meeting -- literally, anything) is via email. I have multiple offices on campus, and it is unlikely that you will find me by simply dropping in outside of a regular office hour, unless we scheduled a meeting ahead of time. So please send me emails.

I receive a lot of email, and I employ automated sorting of my Inbox. If you want your message to be read, the subject of the email ''must'' start with '''PHYS/BIOL212'''. I will be responding to emails related to the class once a day, but not on weekends and holidays. I will be responding more often before major deadlines related to the class. Thus please do not expect a response instantaneously -- plan ahead, and ask questions early. Similarly, if you request a meeting with me in the last minute, I will likely not be available. You need to communicate with me at least a day or two ahead of time if you want to schedule a meeting. Beyond this, I strive to be as responsive as I can be, and to spend as much time as possible with every student who has questions. Please, respect my time: be on time, respond promptly, read emails before sending questions, and I will similarly respect your time.

==About the class==
Computation is one of the pillars of modern science, in addition to experiment and theory. In this course, various computational modeling methods will be introduced to study specific examples derived from physical, biological, chemical, and social systems. We will study how one makes a model, implements it in computer code, and learns from it. We will focus on modeling deterministic dynamics, dynamics with randomness, on comparison of mathematical models to data, and, at the end, on high performance computing. Students will learn Python programming language and will work on computational modeling projects in groups.

There are three goals that I have for students in the class:
#To learn to translate a descriptive problem of a natural phenomenon into a mathematical / computational model.
#To learn how to solve such models using computers, and specifically using the Python programming language. This includes learning how to verify that the solution you produced is a correct solution.
#To learn basic algorithms used in computational science.

In addition, a minor goal of the class is to improve the students' ability to communicate their process of thinking and their results to others. To this extent, the class will require writing project reports, which will be graded on their clarity and completeness.

===Textbooks===
*'''Main Textbook''': J Kinder and P Nelson, ''Student Guide to Python for Physical Modeling'', http://press.princeton.edu/titles/10644.html
::This tutorial is not a complete textbook. I will try to post additional lecture notes online as needed, or to direct you to additional chapters in other textbooks.
:: See also [http://www.wiley.com/WileyCDA/WileyTitle/productCd-EHEP003413.html Computational Modeling and Visualization of Physical Systems with Python] by J Wang and [http://www.physics.purdue.edu/~hisao/book/ Computational Physics] by Giordano and Nakanishi.
::The bible of scientific computing is [http://numerical.recipes Numerical Recipies] by Press et al.

===Required Software===
*[https://www.anaconda.com/download/ Anaconda Python distribution]
*Install Python v 3.X (any minor release v. 3)
Note that coming to class (starting class 2) without a working Python distribution or without a laptop will result in a failing class participation grade.

===Pre-requisites===
Pre-requisites: two semesters of calculus and PHYS 151, or instructor consent. I do not require prior computing experience.

This class differs from most other classes in that we will use mathematical modeling and computer simulations as a language that glues students from very diverse backgrounds. Thus we will be spending many of our class hours ''programming in Python in class''. It is thus essential to have a laptop access ''in class'' and ''for homework". You will be working in groups of 3-4 students, depending on the eventual class enrollment (up to 10 groups in the class), and everyone is required to have laptops and a working Anaconda distribution.

===Class structure===
I request a lot from my students, but also provide them with all the necessary resources to succeed in the class. As a result, students will work hard, but will likely learn more than in a typical class. In practice, this philosophy is implemented as follows.

;Modules: The class will consists of modules of a few weeks long. Typically, each module will consist of traditional in-class lectures or tutorials, where the necessary concepts will be introduced (though we might deviate from this as needed). These will be interspersed with short coding exercises, which you will submit through a provided portal in-class; presence of these will be graded. These are designed to help you grasp the concepts studied in class and to get your feet wet with Python programming. The TAs and the professor will help you in these exercises.

;Labs: A core component of the class are the labs, conducted by the TAs, where you will be solving larger coding/modeling problems, eventually culminating in the final projects for each module, as well as gaining even more experience with Python. The lab problems will start simple, but will become more complex towards the end of the class.

;Quizzes: The last class period of each module will end with a 20-30 min quiz, which will test your comprehension of the material in the module. Barring extraordinary circumstances discussed with me ahead of the quiz class, there will be no makeup quizzes. One worst (or missing) quiz grade will be dropped.

;Reports: You will need to submit reports on projects for each module for grading, multiple times as you are developing these reports over the duration of the module. All the work that you do for in-class coding problems, lab coding projects, and final module projects will need to be completed by you at home, and then submitted for grading. The reports will need to be done using ''Jupyter Notebooks'', and you will submit the notebooks to me via Canvas. Don't worry if you do not know what Jupyter notebook is; we will study this in class. While you can do the programming collectively with other students (I encourage this, in fact), your submissions will be individual. Submissions are due by '''9 am on Monday''' every week (unless Monday is a holiday), starting the first week of class. I will accept '''one late submission''' (up to 48 hours) per student over the course of the semester; you do not need to notify me of a submission delay for this one time. Submissions late by more than 48 hours, or more than one late submission will not be graded and '''will receive a grade of zero''', unless an extension has been requested and granted not later than Friday before the deadline, or there is a documented last-minute emergency.

:The notebooks you submit -- even if they are just progress reports -- must not be rough drafts. Each cell must be executable with no errors, and you must document your code. The notebooks should start with
:#Header: your name, module number, names of other group members.
:For each of the final module reports, Jupyter notebook report should contain the following sections. Each section can be one or multiple cells.
:#Name of the specific project you chose.
:#Short analysis of the problem: Using Scientific American level language, provide a short (few sentences) description of the problem you are solving. Focus on objectives of the study, on what the result of your simulations / analysis will be.
:#Model design: Explain in one paragraph or so how you translate a problem into a computational model. Explain your assumptions and why you made them. Define every symbol you use. Use figures (import them into Jupyter) to illustrate the model and label the diagram of relations among variables.
:#Model solution: This will be the Python code solving the problem per se. Note that the code must be documented -- annotations must explain the general logic of the code, and what specific functions and language constructs do.
:#Results, verification, and conclusion or discussion: Include results (typically numerical values or graphs; importantly, all figures should have titles, axes labels, legends, etc.) of your solution. Explain how you have convinced yourself that the results are valid (that is, how you verified the code). Interpret and explain your results. Explain what, if anything, should have been done differently.

;Partitioning into groups: There will be 5 modules in the class. I expect you to work in groups of 3-4 on each module. You must not be in the same group with any other student more than twice over the course of the semester. Beyond this, please subdivide in your working groups on your own. Notice that no group should be larger than 4 people, but they may be smaller. In fact, you may work on your own if you'd like -- though I don't encourage this.

;Homework: Besides coding problems, discussed above in the ''Reports'' section, there will be no other graded homework sets. However, preparing the reports will require substantial work at home / in the lab.

;Office hours: I will have regular office hours every week. So will the TA (at a different time). In addition, we will have review sessions before the exams, or when it becomes clear that many of you have similar concerns that must be addressed.

;Exams: We will have one '''midterm''' and '''the final exam''' in addition to the quizzes. During these exams, you will be required to answer questions about the concepts we studied in class, as well as to sketch pseudocode or write Python code solving smaller modeling problems. Having a laptop is mandatory during exams. '''Final exam: May 5, 8 am'''

;Laptops: Having a laptop with a working Anaconda installation is mandatory starting the second class.

;Special note: I will need to travel professionally during the semester. As a result, a few classes will be conducted by guest lecturers and/or the TAs. As of the beginning of the semester, I will be away on Feb 19, Mar 4 and possibly Apr 8. I will update the dates of classes that will be taught by guests as I get more informations.

;Updates: Updates will be posted in the News section of the class web site and emailed to the enrolled students through Canvas. It's your responsibility to check your email and the News section the night before each class.

;Weather closures: For ''Short-term University Closures'' (defined as one or two days), changes will be made to the course syllabus to cover the appropriate content during regular class sessions upon return from closure. For "Long-term University Closures" (defined as three or more days), the College has reserved all Registrar scheduled classrooms over the course of two weekends to allow for in-person class meetings to account for the time missed. I will announce these make-up days as needed.

===Grading===
*Lab participation / attendance -- 5%.
**You need to be present at 11 labs (80% of 14 labs) to get the full grade. Please don't inundate the TAs with notes from coaches, doctors, etc. It is your responsibility to make sure that your attendance is recorded by the TA.
*Quizzes -- 15% (cumulative for all modules, one worst/missing quiz grade will be '''dropped''').
*Reports -- 45% (cumulative for all modules, one worst/missing report grade will be '''dropped''' for the final report and cumulative progress). Of these, 25% will be the grades you get for the final reports for each module, and 20% of the grade will be accumulated for the weekly progress sumbissions.
*Midterm -- 15%.
*Final exam -- 20%.

Your scores will convert to a letter grade as follows:
*93.0 - 100 A
*90.0 – 92.9 A-
*87.0 – 89.9 B+
*83.0 – 86.9 B
*80.0 – 82.9 B-
with the pattern repeating for C and D grades; 59.9 or less is a failing grade.

===Honor code===
The Emory College Honor Code applies to all homework assignments.

===Tentative class schedule===
The schedule of topics covered during each lecture is subject to change. I may need to revise it to reflect the pace of the class. The current schedule can be found on the class web site.
Labs start on Jan 16

;Module 1: Introduction to modeling process, Python programming language, Spyder, Jupyter Notebooks, simple plotting. Review of some calculus concepts. Projects Topic: solving an algebraic equation.
::Jan 15, 22, 27, 29, Feb 3
::Feb 3: Quiz 1
::''Progress Report: Jan 27, Feb 3''
::''Final Report: Feb 10''
;Module 2: Modeling dynamics of systems described by multiple variables, computational errors, simulation techniques for deterministic dynamics, Python functions, modules, and scopes, advanced plotting. Project Topics: solving systems of coupled differential equations describing various natural phenomena.
::Feb 5, 10, 12, 17, 19
::Feb 19: Quiz 2
::''Progress Report: Feb 17''
::''Final Report: Feb 24''
;Module 3: Data Driven Models -- Fitting Models to Data: Linear regression and other empirical models, optimization and optimization methods, curve fitting. Project Topics: fitting nonlinear curves to experimental data.
::Feb 24, 26, Mar 2, 4, 16
::''Mar 9, 11: Spring break, no classes''
::Mar 16: Quiz 3
::''Progress Reports: Mar 2, 16''
::''Final Report: Mar 23''
;Mar 18 -- Midterm
;Module 4: Simulations with Randomness, random numbers and random walks, cellular automata and agent-based models. Project Topics: pattern formation in stochastic systems.
::Mar 25, 30, Apr 1, 6, 8
::Apr 8: Quiz 4
::''Progress Reports: Mar 30, Apr 6''
::''FInal Report: Apr 13''
;Module 5: High Performance Computing. Project topics: solving partial differential equations on multiple cores.
::Apr 13, 15, 20, 22
::Apr 27: Quiz 5
::''Progress Reports: Apr 20''
::''Final Report: Apr 27''
;Apr 27 -- catch-up class; exam review.
;'''May 5, 8:00 am -- Final Exam'''

===Statement from the Department of Physics===
Please treat your classmates with respect both in and out of the classroom. It is unacceptable to discriminate against your fellow students on the basis of race, gender, perceived physics acumen, or any other reason. If you have any concerns, please let me know or contact the department chair, Prof. Stefan Boettcher.

===COVID-19 related changes===

;Summary: the course will run largely in an asynchronous manner, save for lectures and labs that will turn into large discussion sessions and working-together sessions. You will need to do work reading for lectures before they start.

;Lectures: I will make an effort of having my lecture notes at least 24 hours ahead of our regularly scheduled class times (MW, 10am EDT), posted on the course web site. I will not be recording video lectures, as these will be largely redundant with my lecture notes. For every lecture, I will post a questionnaire, which you will need to answer after reading the lecture materials, and at least an hour before the class time. I will use your answers to see which parts of the lecture are less clear for you, and adjust my teaching plan accordingly.

;Class sessions: (MW, 10am-11:15am EDT) These will be flipped — in the sense that I will not be delivering lectures, but only responding to your questions that emerge from pre-lecture questionnaires, and during the lectures. I expect you to attend these lectures, and have video on (I tried to work with video off, but it’s hard without getting the facial expression feedback), however, I will not be grading on attendance — especially because many of you are now scattered over various time zones across the world. Thus, to get the most out of these sessions, you should come prepared — having read the material, and having formulated questions. Class sessions will be recorded and posted on the course web site. The College has asked me to add the following information to the syllabus:

:::Lectures and other classroom presentations presented through video conferencing and other materials posted on Canvas are for the sole purpose of educating the students enrolled in the course. The release of such information (including but not limited to directly sharing, screen capturing, or recording content) is strictly prohibited, unless the instructor states otherwise. Doing so without the permission of the instructor will be considered an Honor Code violation, and may also be a violation of state or federal law, such as the Copyright Act. All University policies remain in effect for students participating in remote education.

;Quizzes and Midterm: These will be asynchronous, not in class time. The due dates for Quiz 3 will be March 24 at 10am (the quiz will open on Sunday night, and you will have 30 minutes to do it on your own time). The due date for the Midterm will be March 26 at 10am (the midterm will open on Tuesday, and you will have 2 hours between when you download it and when you submit the result). I will communicate the deadlines for other quizzes later.

;Final: Final will be asynchronous, you will be taking it on your own time. I don’t know when yet, and am waiting for instructions from the College.

;Labs: The TAs will let you know their specific instructions for the labs. Generally, the labs will be big discussion sessions, where you work in groups, in breakout rooms, on the code in the lab notebooks. Lab participation will not be graded from now on — the entire lab participation grade will be based on the first half of the semester.

;Grading: All of the grading policies remain the same except that the 5% lab participation grade will be split into: 2.5% for lab participation through the spring break and 2.5% for answering pre-lecture questionnaires for after the spring break.

;Schedule: The semester is not being extended. This means that we lost two lecture classes over the course of the break. I do not know yet how we will catch up with those, and whether we will. Let’s see how the first week shapes up, and I will let you know later.