Team:Paris/Modeling/Roadmap

From 2008.igem.org

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You have reach to our roadmap, where we indicate our goals and the foreseen schedule.
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**Other interactions to increase the robustness
**Other interactions to increase the robustness
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===July===
===July===

Revision as of 18:10, 12 August 2008

You have reach to our roadmap, where we indicate our goals and the foreseen schedule.

Contents

Roadmap

  • Aims of the modeling part
  • First approach proposed
    • Hill functions
    • first model + score function
    • bibliography
    • findparam
    • experiments
  • Second approach
    • bibliography
    • equations
    • results
    • experiments
  • 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

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

  • On the previous model
    • add cells
    • have a population that changes over time
    • Parameters robustness (threshold, Pa) (screening)
    • Gillespie : rebuild the model with this new approach // noise
    • Quantification of FIFO (see Yann)
    • Quantification period (influent parameters...)
  • Other ideas
    • biocham : comparison with adapted repressilator
    • system to add "random" links for model optimisation (quantification of quality : see that oscillation FIFO and synchronization still occur)
    • change place of tetR (on flgA...)
    • see mgs (gillespie or spatialization)
    • highly rigorous model with mRNA and ON/OFF