Team:Paris/Modeling/Roadmap

From 2008.igem.org

(Difference between revisions)
(August)
(Todo)
Line 20: Line 20:
==Todo==
==Todo==
-
===Design a modular Matlab modelisation of our system===
+
* Continue the previous model
-
Using the following approach:
+
    ** Synchronyzation
-
* 3 modules corresponding to the FIFO Temporal Order function, the Oscillation's one and the Sync function.
+
    ** Estimation of the FIFO processes
-
* Gather the 3 modules using a blackbox approach: each function is a box having its own inputs and outputs and does not interact with the others.
+
    ** Stochastic modeling (Gilespie)
-
* Divide each box in smaller parts that we can quickly try in the wet lab to figure out precisely some missing parameters.
+
-
===Implement the same models in BIOCHAM===
+
*Test of robustness
-
It will allow easier:
+
    **repressilator
-
* Exploration of the paramaters space
+
    ** comparison
-
* Evalution of the robustness
+
 
-
* Changes (to a stochastic model for example)
+
*Enhancing the system
 +
    **Better FIFO behaviour
 +
    **Other interactions to increase the robustness
-
===MGS===
 
-
* Understand the syntax!
 
-
* Develop a 3D model to simulate diffusion even if the medium will in fact be shook.
 
|}<br style="clear:both" />
|}<br style="clear:both" />

Revision as of 13:31, 6 August 2008

Contents

Calendar

July

  • 07/31 - Have a full bibliography ⇒ DONE

August

  • 06/07 - First model of the FIFO temporal order, of the backward control inducing the oscillations ⇒ DONE
  • 08/07 - Model the synchronization between cells, using Biocham
  • 08/15 - Summary about the ODE method, Space introduction into models (AC, Delaunay)
  • 08/22 - Feedback: list missing things (parameters), Optimization, Robustness analysis

September

  • 09/22- Checkpoint meeting

October

  • 10/15 - Scheduled wiki ending (2 weeks before the real ending to finish details)
  • 10/31 - Official wiki ending (date to be checked)

Todo

  • Continue the previous model
   ** Synchronyzation
   ** Estimation of the FIFO processes
   ** Stochastic modeling (Gilespie) 
  • Test of robustness
   **repressilator
   ** comparison 
  • Enhancing the system
   **Better FIFO behaviour
   **Other interactions to increase the robustness