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A1 : Due by 11:30 AM, Oct. 1 via Catalyst

  1. Read the articles in the special issue of Science on Synthetic Biology and answer the following. (a) Describe a potential clinical application of synthetic biology. (b) Describe potential biofuel application: what kind of fuel, and why is it hard to produce with engineered cells? (c) Describe a way the authors suggest that synthetic biology should be regulated and why or why not this should be done.
  2. Download and install gro. Try running the various examples. Next, find the edge.gro and run it a few times. What does it do? Make a copy of it called newedge.gro and open it in an editor of some kind (see the documentation). In newedge.gro, change the parameter st on line 35 to 0.3, and then load and run the simulation to 1000 cells. How is the resulting behavior different? Try again with st equal to 0.1. Describe the effect of changing this variable. Finally, make a figure illustrating the effect graphically by using snapshots from the simulation (or screen grabs). Note that we will make heavy use of gro later in this class. For now, just see if you can run it and if you'd like to know more, read this paper.
  3. We will use some kind of mathematical software during this course and this exercise is designed to make sure you have access to and more or less know how to use such a software package. To this end, obtain and install a copy of MATLAB, Mathematica, R, or some similar program. Generate a list of 100 random numbers between 0 and 1 and plot a histogram of the resulting list. Show your code, the histogram, and explain why you chose the software you chose.
  4. Extra credit: Modify newedge.gro so that, after 1000 cells, gro writes the rfp/volume values, over all cells, to a file. Read them into your mathematical software (i.e. MATLAB, Mathematica, R, or whatever) and plot a histogram of the results. What accounts for the variation?

Turn in Assignment 1 here: https://catalyst.uw.edu/collectit/assignment/koishi/23996/95633.