Team:Paris/Modeling/Roadmap

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{{Paris/Menu}}
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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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* Aims of the modeling part
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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
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**bibliography
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**equations
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**results
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**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 ==
*[[Team:Paris/July 7|07/31]] - Have a full bibliography  ⇒ '''DONE'''
*[[Team:Paris/July 7|07/31]] - Have a full bibliography  ⇒ '''DONE'''
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===August===
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== August ==
*[[Team:Paris/August 6|06/07]] - First model of the FIFO temporal order, of the backward control inducing the oscillations ⇒ '''DONE'''
*[[Team:Paris/August 6|06/07]] - First model of the FIFO temporal order, of the backward control inducing the oscillations ⇒ '''DONE'''
*[[Team:Paris/August 8|08/07]] - Model the synchronization between cells, using Biocham  
*[[Team:Paris/August 8|08/07]] - Model the synchronization between cells, using Biocham  
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*[[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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= Notebook =
* On the previous model
* On the previous model
** add cells
** add cells
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** Quantification of FIFO (see Yann)
** Quantification of FIFO (see Yann)
** Quantification period (influent parameters...)
** Quantification period (influent parameters...)
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* End the Hill model design
* Other ideas
* Other ideas
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** change place of tetR (on flgA...)
** change place of tetR (on flgA...)
** see mgs (gillespie or spatialization)
** see mgs (gillespie or spatialization)
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** highly rigorous model with mRNA and ON/OFF
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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)
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==Bonus ideas==
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* optimization of the links in a bio process
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* new way to see modeling (stochastic / ON&OFF + mRNA...)
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* new way to model noise
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* using the noise?
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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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