Team:Paris/Modeling/Roadmap

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* You have reached to our roadmap, where we indicate our goals and the foreseen schedule. This page is of the utmost importance for the team coordination, since we use it as well as a notebook, where we store the ideas we are liable to have... We thus apologize for the occasional mess...
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==Calendar==
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===July===
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=Roadmap=
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*[[Team:Paris/July 7|07/31]] - Have a full bibliography
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===August===
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* Aims of the modeling part
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*[[Team:Paris/August 7|08/07]] - First model of the FIFO temporal order, of the backward control inducing the oscillations and of the synchronization between cells, using Biocham (or eventually Dizzy)
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* First approach proposed
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** Hill functions
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** first model + score function
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** bibliography
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** findparam
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**experiments
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*Second approach
 +
**bibliography
 +
**equations
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**results
 +
**experiments
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* Continue the previous model
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**Synchronization
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**Estimation of the FIFO processes
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**Stochastic modeling (Gilespie)
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*Test of robustness
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**repressilator
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**comparison
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*Enhancing the system
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**Better FIFO behaviour
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**Other interactions to increase the robustness
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= Calendar =
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== July ==
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*[[Team:Paris/July 7|07/31]] - Have a full bibliography ⇒ '''DONE'''
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== August ==
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*[[Team:Paris/August 6|06/07]] - First model of the FIFO temporal order, of the backward control inducing the oscillations ⇒ '''DONE'''
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*[[Team:Paris/August 8|08/07]] - Model the synchronization between cells, using Biocham  
*[[Team:Paris/August 15|08/15]] - Summary about the ODE method, Space introduction into models (AC, Delaunay)
*[[Team:Paris/August 15|08/15]] - Summary about the ODE method, Space introduction into models (AC, Delaunay)
*[[Team:Paris/August 22|08/22]] - Feedback: list missing things (parameters), Optimization, Robustness analysis
*[[Team:Paris/August 22|08/22]] - Feedback: list missing things (parameters), Optimization, Robustness analysis
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===September===
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== September ==
*[[Team:Paris/September 22|09/22]]- Checkpoint meeting
*[[Team:Paris/September 22|09/22]]- Checkpoint meeting
===October===
===October===
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*[[Team:Paris/October 31|10/31]] - Official wiki ending (date to be checked)
*[[Team:Paris/October 31|10/31]] - Official wiki ending (date to be checked)
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==Todo==
 
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===Design a modular Matlab modelisation of our system===
 
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Using the following approach:
 
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* 3 modules corresponding to the FIFO Temporal Order function, the Oscillation's one and the Sync function.
 
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* 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.
 
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* Divide each box in smaller parts that we can quickly try in the wet lab to figure out precisely some missing parameters.
 
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===Implement the same models in BIOCHAM===
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= Notebook =
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It will allow easier:
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* On the previous model
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* Exploration of the paramaters space
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** add cells
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* Evalution of the robustness
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** have a population that changes over time
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* Changes (to a stochastic model for example)
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** Parameters robustness (threshold, Pa) (screening)
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** Gillespie : rebuild the model with this new approach // noise
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** Quantification of FIFO (see Yann)
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** Quantification period (influent parameters...)
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* End the Hill model design
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===MGS===
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* Other ideas
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* Understand the syntax!
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** biocham : comparison with adapted repressilator
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* Develop a 3D model to simulate diffusion even if the medium will in fact be shook.
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** system to add "random" links for model optimisation (quantification of quality : see that oscillation FIFO and synchronization still occur)
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|}<br style="clear:both" />
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** change place of tetR (on flgA...)
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** see mgs (gillespie or spatialization)
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** highly rigorous model with mRNA
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** Evaluation of the qulity of a model (/accuracy concerning the real evolution & / parameters you have to find)

Latest revision as of 13:53, 28 August 2008


  • You have reached to our roadmap, where we indicate our goals and the foreseen schedule. This page is of the utmost importance for the team coordination, since we use it as well as a notebook, where we store the ideas we are liable to have... We thus apologize for the occasional mess...

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
    • Synchronization
    • 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)


Notebook

  • 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...)
  • End the Hill model design
  • 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
    • Evaluation of the qulity of a model (/accuracy concerning the real evolution & / parameters you have to find)
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