Physics 434, 2014: Projects

From Ilya Nemenman: Theoretical Biophysics @ Emory
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Back to Physics 434, 2014: Information Processing in Biology.

Please choose a project you will be working on ASAP. Work in groups of 3-4 people. Your simulation codes can be written jointly, but your final report should be your own.

In-class presentation

This is a collective presentation. Aim for about 20-25 minutes, and it will probably take you 30-40 when all the questions that the rest of the class will be asking are factored in. Presentation should start with explaining the problem -- what is being tested? why? what is the data? why is this interesting? Then you need to spend a few slides on the methods that you used. Don't show the code itself -- nobody can read it on-screen in real time. Instead, try to explain the flow of your algorithm, what it does, and how. Then move on to the findings, and finally to a summary.

Make sure that all members of your team participate in writing the presentation, in presenting different aspects of it in-class, and have approved all of it, before you present it. View the presentation as not a final result (your report will be your final result), but as an advanced summary of what you are doing. The feedback from other students and from me will help you to identify what is missing, and what you did well. You should have something to say when you present, but remember that there's quite some time between the presentation and when the final report is due, so a lot will probably change in your mind over that period of time.

Remember, that we are in a physics class. Now hand-waving, no trends -- only exact numbers work.

The project report

A big part of your final grade is the project report. This should be done individually by every student. (Note that in an earlier version, it said by mistake it shouldn't be done individually, in contrary to what I said in class many times. My apologies for the error. Please talk to me if this has caused any confusion.) This shouldn't be an opus magnum -- ten pages of text, results, plots, etc. would be quite sufficient. Even 5-7 pages could be fine, depending on how well you do them. Make sure you explain everything that you did -- after reading your report, I need to understand that you personally (not just the other members of your team) understand what's going on. Your explanations need to be mathematical, and rigorous. No need for verbiage, no need for essays -- a mathematical formula tells me a lot more than a page of words. As you are reading articles for your projects, see how they are written; this will help you in writing your own report as well.

Structure your report as you would structure a scientific paper: title, abstract, introduction to the problem, methods used for solving the problem, results, and conclusions/discussion. Pay particular attention to the introduction of the problem, and make sure it explains in detail what you do in this report, and, crucially, why it's an interesting problem and how it is positioned in the bigger picture of the class and the topic areas it covered.