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Team:ETHZ Basel/Modeling/Light Switch
From 2010.igem.org
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## Plot Figure 6a & 7a from [[Team:ETHZ Basel/Modeling/Sorokina2009#References|[1]]] - <span style="color:#006400;"> OK </span> | ## Plot Figure 6a & 7a from [[Team:ETHZ Basel/Modeling/Sorokina2009#References|[1]]] - <span style="color:#006400;"> OK </span> | ||
# Adapt model to experimental setup - <span style="color:#FF0000;"> Problems </span> | # Adapt model to experimental setup - <span style="color:#FF0000;"> Problems </span> | ||
| - | # Link model to chemotaxis ODE models | + | # Link model to chemotaxis ODE models - <span style="color:#FF0000;"> Problems </span> |
== Status == | == Status == | ||
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* (7/31): (SVN rev. 6) first attempts to set light-conditions according to experimental setups (Goal 2) | * (7/31): (SVN rev. 6) first attempts to set light-conditions according to experimental setups (Goal 2) | ||
* (8/03): (SVN rev. 7) simplifications, control of all equations and parameters (Goal 2) | * (8/03): (SVN rev. 7) simplifications, control of all equations and parameters (Goal 2) | ||
| + | * (8/07): (SVN rev. 8) first try to connect light-switch to chemotaxis model (Goal 3) | ||
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== Tasks == | == Tasks == | ||
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| [[Image:Fig6a_rev6_experimental.png|thumb|400px|'''Figure 6a]] || [[Image:Fig7a_rev6_experimental.png|thumb|400px|'''Figure 7a]] | | [[Image:Fig6a_rev6_experimental.png|thumb|400px|'''Figure 6a]] || [[Image:Fig7a_rev6_experimental.png|thumb|400px|'''Figure 7a]] | ||
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| + | === Goal 3 === | ||
| + | |||
| + | I tried to connect this model to the Mello2003 chemotaxis model. This was done simply by feeding the output of Sorokina2009 to Mello2003. Several problems occured: | ||
| + | |||
| + | # ODEs are numerically solved in both models individually. Therefore, results from one model can not be simply put into the other, due to different time-scales. A quick first bugfix was done, by taking the closest time-step. | ||
| + | # Problem of Goal 2 is still present and affects results of Goal 3. | ||
== References == | == 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.] | [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.] | ||
Revision as of 14:56, 7 August 2010
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
- Implement original model
- Plot Figure 6a & 7a from [1] - OK
- Adapt model to experimental setup - Problems
- Link model to chemotaxis ODE models - Problems
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)
- (7/28): (SVN rev. 5) original model partly implemented, so far working: Goal 1.1 reached
- (7/31): (SVN rev. 6) first attempts to set light-conditions according to experimental setups (Goal 2)
- (8/03): (SVN rev. 7) simplifications, control of all equations and parameters (Goal 2)
- (8/07): (SVN rev. 8) first try to connect light-switch to chemotaxis model (Goal 3)
Tasks
- Verification & Discussion
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.
Results
Goal 1
The original model was partly implemented and corresponding qualitative plots 6a and 7a have been computed.
 |  |
Goal 2
Light conditions were set according to first thoughts in Spiro and Mello models. Unfortunately, this doesn't result in usable concentration changes. There is possibly a bug somewhere, or we have to redefine the experimental setup.
 |  |
Goal 3
I tried to connect this model to the Mello2003 chemotaxis model. This was done simply by feeding the output of Sorokina2009 to Mello2003. Several problems occured:
- ODEs are numerically solved in both models individually. Therefore, results from one model can not be simply put into the other, due to different time-scales. A quick first bugfix was done, by taking the closest time-step.
- Problem of Goal 2 is still present and affects results of Goal 3.
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.]
