Modelling Notebook

Week 1 08/06/09 - 12/06/09

• We split into pairs and began writing a system of ODEs for each of our three possible wiring diagrams. The aim of this was to decide which genetic circuitry would work best, depending on how the models performed. In order to get any data out the models however we had to ask the biologists on the team to help us find parameters, although this proved to be challenging.
• Started to program our ODE's into our RK4 program (written in C)

Week 2 15/06/09 - 19/06/09

• It became apparent, from the modeling, that the third circuit design was superiour to the other two for several reasons. As such the biologists could start thinking about starting their lab work.

Week 3 22/06/09 - 26/06/09

• First proper chemotaxis model’s created without animation, and could only handle a few bacteria at a time Consideration went into more practical sides of the chemotaxis, such as average time to travel a distance. Bacteria respond to a concentration, as opposed to distance.

Week 4 29/06/09 - 03/07/09

Week 5 05/07/09 - 10/07/09

Week 6 13/07/09 - 16/07/09

Week 7 20/07/09 - 24/07/09

Week 8 27/07/09 - 31/07/09

Week 9 03/08/09 - 07/08/09

Week 10 10/08/09 - 14/08/09

Week 11 17/08/09 - 21/08/09

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