Team:ETHZ Basel/Modeling/SorokinaMello

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(New page: {{Template:ETHZ_Basel10}} = 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 ...)
 
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{{Template:ETHZ_Basel10}}
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= Modeling of the light-input, light-output system =
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= Light-input system coupled to chemotaxis model (Sorokina/Mello) =
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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:  [[Team:ETHZ Basel/Modeling/Sorokina2009#References|[1]]].
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The Sorokina model will be coupled to the Mello model. This is done by expanding the single molecular models to a single DAE model.
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At the moment, the implementation is not working.
== Goals ==
== Goals ==
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# Implement original model
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# Link model to Mello chemotaxis ODE models
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## Plot Figure 6a & 7a from [[Team:ETHZ Basel/Modeling/Sorokina2009#References|[1]]] - <span style="color:#006400;"> OK </span>
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# Define experimental conditions
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# Adapt model to experimental setup - <span style="color:#006400;"> OK </span>
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# Link model to chemotaxis ODE models
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== Status ==
== Status ==
Please find the current version on the SVN-Server.
Please find the current version on the SVN-Server.
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* (7/25): (SVN rev. 3) start development by George
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* (8/12): (SVN rev. 15) Goal 1 in progress
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* (7/27): (SVN rev. 4) original model partly implemented, not yet working (Goal 1.1)
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* (8/14): (SVN rev. 16) Goal 1 in progress
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* (7/28): (SVN rev. 5) original model partly implemented, so far working: Goal 1.1 reached
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* (8/15): (SVN rev. 17) Goal 1 in progress
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* (7/31): (SVN rev. 6) first attempts to set light-conditions according to experimental setups (Goal 2)
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* (8/03): (SVN rev. 7) simplifications, control of all equations and parameters (Goal 2)
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* (8/07): (SVN rev. 8) first try to connect light-switch to chemotaxis model (Goal 3)
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* (8/10): (SVN rev. 10) goal 2 reached (Goal 2)
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== Tasks ==
== Tasks ==
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* Fix the implementation
* Verification & Discussion
* Verification & Discussion
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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.
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I will continue to work on this model. If you would like to help, please check the SVN server for the current version and send me an email regarding your participation.
== Results ==
== Results ==
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=== Goal 1 ===
=== Goal 1 ===
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The original model was partly implemented and corresponding qualitative plots 6a and 7a have been computed.
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Please see SVN Rev. 17 for first try: ./SorokinaMello
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{| border="0"
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| [[Image:Fig6a_rev5.png|thumb|400px|'''Figure 6a]] || [[Image:Fig7a_rev5.png|thumb|400px|'''Figure 7a]]
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|}
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=== Goal 2 ===
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Light conditions were set according to first thoughts in Spiro and Mello models. Now it works!
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{| border="0"
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| [[Image:Fig1_rev10_experimental.png|thumb|400px|'''Figure 1]] || [[Image:Fig2_rev10_experimental.png|thumb|400px|'''Figure 2]]
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|-
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| [[Image:Fig3_rev10_experimental.png|thumb|400px|'''Figure 3]] || [[Image:Fig4_rev10_experimental.png|thumb|400px|'''Figure 4]]
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|}
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=== Goal 3 ===
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This will be done in the next few days.
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== 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.]

Latest revision as of 15:15, 15 August 2010

Light-input system coupled to chemotaxis model (Sorokina/Mello)

The Sorokina model will be coupled to the Mello model. This is done by expanding the single molecular models to a single DAE model.

At the moment, the implementation is not working.

Goals

  1. Link model to Mello chemotaxis ODE models
  2. Define experimental conditions

Status

Please find the current version on the SVN-Server.

  • (8/12): (SVN rev. 15) Goal 1 in progress
  • (8/14): (SVN rev. 16) Goal 1 in progress
  • (8/15): (SVN rev. 17) Goal 1 in progress

Tasks

  • Fix the implementation
  • Verification & Discussion

I will continue to work on this model. 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

Please see SVN Rev. 17 for first try: ./SorokinaMello

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.]

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