Team:Paris/Modeling/Roadmap

From 2008.igem.org

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(Bonus ideas)
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==Todo==
==Todo==
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* Continue the previous model
+
* On the previous model
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** Synchronyzation
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** add cells
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** Estimation of the FIFO processes
+
** have a population that changes over time
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** Stochastic modeling (Gilespie)  
+
** Parameters robustness (threshold, Pa) (screening)
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*Test the robustness
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** Gillespie : rebuild the model with this new approach // noise
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**repressilator
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** Quantification of FIFO (see Yann)
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** comparison  
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** Quantification period (influent parameters...)
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*Enhance the system
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**Better FIFO behaviour
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* Other ideas
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**Other interactions to increase the robustness
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** 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
==Bonus ideas==
==Bonus ideas==

Revision as of 17:49, 8 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

  • 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

Bonus ideas

  • optimization of the links in a bio process
  • new way to see modeling (stochastic / ON&OFF + mRNA...)
  • new way to model noise
  • using the noise?