"

From 2010.igem.org

Modeling of the light-input, light-output system

The light-input, light-output system PIF3-PhyB will be used to control spatial localization of key-proteins from chemotaxis. A model will be implemented according to a recent publication: [1].

Goals

1. Implement original model
   1. Plot Figure 6a from [1]
2. Link model to chemotaxis ODE models
3. Adapt model to experimental setup

Status

Please find the current version on the SVN-Server.

• (7/25): (SVN rev. 3) start development by George
• (7/27): (SVN rev. 4) original model partly implemented, not yet working (Goal 1.1)

Tasks

• Help wanted to fix original model implementation

Results

I tried to plot the Figure 6a, but the ode15s will crash. I guess, there's a stiffness problem to be solved. Possible other problems could be the assumptions I made in model.m. The original paper mixes the nomenclature of the variables, so there could be some errors.

I will continue to work on this model the whole week. If you would like to help, please check the SVN server for the current version. And send me an email regarding your participation.

References

[1] [http://www.jbioleng.org/content/3/1/15 Sorokina et al: A switchable light-input, light-output system modelled and constructed in yeast. J Biol Eng. 2009 Sep 17;3:15.]