Physics 212, 2019: Syllabus - Revision history

Ilya: /* Class structure */

2019-02-03T20:35:18Z

‎Class structure

Ilya: /* Grading */

2019-02-03T20:33:08Z

‎Grading

Ilya: /* Tentative class schedule */

2019-01-28T12:52:48Z

‎Tentative class schedule

Ilya at 16:49, 23 January 2019

2019-01-23T16:49:32Z

Ilya at 03:48, 23 January 2019

2019-01-23T03:48:51Z

Ilya: /* Tentative class schedule */

2019-01-16T04:13:37Z

‎Tentative class schedule

Ilya: /* Tentative class schedule */

2019-01-16T04:11:47Z

‎Tentative class schedule

Ilya: /* Class structure */

2019-01-16T04:11:16Z

‎Class structure

Ilya: /* Statement from the Department of Physics */

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‎Statement from the Department of Physics

Ilya: /* Tentative class schedule */

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‎Tentative class schedule

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 ;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 a report on projects for each module for grading. This will be due by the end of the weekend following end of the module. While you can do the programming / model development work collectively with other students in your group, the quizzes and the reports are individual. The reports will need to be done using ''Jupyter Notebooks'', and you will submit the notebooks to me via email. Don't worry if you do not know what Jupyter notebook is; we will study this in class. Submissions are due by '''9 am on Monday''' on the weeks indicated in the syllabus. I will accept '''one late submission''' (up to 48 hours) per student over the course of the semester. 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.
+;Reports: You will need to submit a report on projects for each module for grading. This will be due by the end of the weekend following end of the module. While you can do the programming / model development work collectively with other students in your group, the quizzes and the reports are individual. 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. Submissions are due by '''9 am on Monday''' on the weeks indicated in the syllabus. I will accept '''one late submission''' (up to 48 hours) per student over the course of the semester. 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.
 :Each Jupyter notebook report should contain the following sections. Each section can be one or multiple cells.
@@ Line 61: / Line 61: @@
 :#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: 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.
+:#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. You will 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.

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 **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''').
-*Project reports -- 40% (cumulative for all modules, one worst/missing report grade will be '''dropped''').
+*Project reports -- 40% (cumulative for all modules, one worst/missing report grade will be '''dropped'''). Note that 10% of the project grade (4% of the total grade) will be determined simply by submitting your project choices and student group membership on time.
 *Midterm -- 15%.
 *Final exam -- 20%.

@@ Line 104: / Line 104: @@
 ;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 16, 23, 24, 28, 30, Feb 4
+::Jan 16, 23, 28, 30, Feb 4
 ::Feb 4: Quiz 1
 ::''Project report due: Feb 11''

@@ Line 11: / Line 11: @@
 :Ilya Nemenman --  Monday 11:30-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
 :TA Qihan Liu -- Friday, 2:00-3:00, MSC N117E
-:TA Jian Wang -- Wednesday, 2:00-3:00, MSC N118E
+:TA Jian Wang -- Wednesday, 2:00-3:00, MSC N118D
 ;Class Web Page: http://nemenmanlab.org/~ilya/index.php/Physics_212,_2019:_Computational_Modeling_For_Scientists_And_Engineers

@@ Line 9: / Line 9: @@
 ;TA: Jian Wang jian.wang2@emory.edu
 ;Office Hours
-:Ilya Nemenman --  Monday 11:30-1:00, and by appointment, MSC N240
+:Ilya Nemenman --  Monday 11:30-1:00 (subject to change), and by appointment, MSC N240 or N117A if too many people.
-:Qihan Liu -- TBA
+:TA Qihan Liu -- Friday, 2:00-3:00, MSC N117E
-:Jian Wang -- TBA
+:TA Jian Wang -- Wednesday, 2:00-3:00, MSC N118E
 ;Class Web Page: http://nemenmanlab.org/~ilya/index.php/Physics_212,_2019:_Computational_Modeling_For_Scientists_And_Engineers

@@ Line 111: / Line 111: @@
 ::Feb 25: Quiz 2
 ::''Project report due: Mar 4''
-;Module 3: Data Driven Models -- Fitting Models to Data: Linear regression and other empirical models, optimization and optimization methods, curve fitting.
+;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 27, Mar 4, 6, 20, 25
 ::''Mar 11, 13: Spring break, no classes''
@@ Line 117: / Line 117: @@
 ::''Project report due: Apr 1''
 ;Mar 18 -- Midterm
-;Module 4: Simulations with Randomness, random numbers and random walks, cellular automata and agent-based models.
+;Module 4: Simulations with Randomness, random numbers and random walks, cellular automata and agent-based models. Project Topics: pattern formation in stochastic systems.
 ::Mar 27, Apr 1, 3, 8, 10
 ::Apr 10 Quiz 4
 ::''Project report due: Apr 15''
-;Module 5: High Performance Computing
+;Module 5: High Performance Computing. Project topics: solving partial differential equations on multiple cores.
 ::Apr 15, 17, 22, 24
 ::Apr 24: Quiz 5

@@ Line 56: / Line 56: @@
 ;Reports: You will need to submit a report on projects for each module for grading. This will be due by the end of the weekend following end of the module. While you can do the programming / model development work collectively with other students in your group, the quizzes and the reports are individual. The reports will need to be done using ''Jupyter Notebooks'', and you will submit the notebooks to me via email. Don't worry if you do not know what Jupyter notebook is; we will study this in class. Submissions are due by '''9 am on Monday''' on the weeks indicated in the syllabus. I will accept '''one late submission''' (up to 48 hours) per student over the course of the semester. 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.
-:Each Jupiter notebook report should contain the following sections. Each section can be one or multiple cells.
+:Each Jupyter notebook report should contain the following sections. Each section can be one or multiple cells.
 :#Header: your name, report title, names of other group members.
 :#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.

← Older revision		Revision as of 04:11, 16 January 2019
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	===Statement from the Department of Physics===		===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. ~~Eric Weeks (erweeks@emory.edu)~~.	+	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.

@@ Line 119: / Line 119: @@
 ;Module 4: Simulations with Randomness, random numbers and random walks, cellular automata and agent-based models.
 ::Mar 27, Apr 1, 3, 8, 10
-::Apr 15 Quiz 4
+::Apr 10 Quiz 4
-::''Project report due: Apr 23''
+::''Project report due: Apr 15''
 ;Module 5: High Performance Computing
-::Apr 16, 18, 23, 25, 30
+::Apr 15, 17, 22, 24
-::Apr 30: Quiz 5
+::Apr 24: Quiz 5
-::''Project report due: May 2'' -- '''Notice the special day!'''
+::''Project report due: Apr 29''
-;'''May 7, 8:00 am -- Final Exam'''
+;Apr 29 -- catch-up class; exam review.
 ===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. Eric Weeks (erweeks@emory.edu).