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A8 : Due Dec. 12


Come up with a gro simulation of an interesting system that you design. The only real requirement is that the system use signals and geometry or position in some way (otherwise why use gro?). Examples that are motivated by interesting biology or biotechnology, that have some hope of ever being built, or that illustrate an important concept are ideal. You should produce:

  1. A YouTube video, uploaded to soslab.general, of no more than 3 minutes in length. You can add sound, such as a narrative if you want. The videos should at the very least have a title slide with your name, the name of the video, the name of the course, and a link to the gro webpage. Even better would be to include a diagram of your system and some explanation of what is going on before the simulation begins. And even better would be actual data plotted in some nice way showing how your system works over many simulations, for example. At the end, credits would be good in case you used ideas of collaborators and/or classmates.
  2. A paragraph description of your system that would also be included on the YouTube page.
  3. The code used to generate the simulation, with comments to explain what it does and how to tweak parameters, for example.


For each day of graduate student presentations, choose one presentation and write a paragraph that (a) summarizes the work, and (b) describes an idea of how to take the work forward by improving upon it, asking a follow question, or applying it to some application.


In addition to your presentation, you must turn in a written report of the paper of no more than two pages. Reports should by brief and address the following:

  1. What is the background or context of the paper?
  2. What is the main contribution of the paper?
  3. How do the results in the paper address at least one of the "five hard truths"?
  4. What would you do with the paper going forward by improving upon it, asking a follow question, or applying it to some application?

Instructions for turning in your assignment

Instructions for uploading youtube videos to the soslab.general channel will be emailed to the class.
Turn in written reports here: