Team:Paris/Modeling

From 2008.igem.org

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===Roadmap===
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=Roadmap=
* Aims of the modeling part
* Aims of the modeling part
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If you want to have a look at our modeling notebook: [[Team:Paris/Modeling/Roadmap|Notebook]]
If you want to have a look at our modeling notebook: [[Team:Paris/Modeling/Roadmap|Notebook]]
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===Presentation of our work===
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=Presentation of our work=
The different phases of our modeling work...
The different phases of our modeling work...
The following presentation is not necessarly chronological, but presents the advantage of introducing our work from the simplest model to the most complicated.
The following presentation is not necessarly chronological, but presents the advantage of introducing our work from the simplest model to the most complicated.
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==== I - Linear Approach ====
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== I - Linear Approach ==
An [[Team:Paris/Modeling/linear_approach|Oscillatory Biological Model]], with almost only linear relationships.
An [[Team:Paris/Modeling/linear_approach|Oscillatory Biological Model]], with almost only linear relationships.
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==== II - "Hill" Approach ====
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== II - "Hill" Approach ==
That was our [[Team:Paris/Modeling/hill_approach|first approach]], which we would like to study as far as possible. The [[Team:Paris/Modeling#III_-_Estimation_of_Paramaters|estimation of parameters]] is mostly for this one.
That was our [[Team:Paris/Modeling/hill_approach|first approach]], which we would like to study as far as possible. The [[Team:Paris/Modeling#III_-_Estimation_of_Paramaters|estimation of parameters]] is mostly for this one.
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We use mostly ''Hill functions'' to describe relationships between ''transcription factors'' and promoters, and do no take into acount the ''translations'' phase.
We use mostly ''Hill functions'' to describe relationships between ''transcription factors'' and promoters, and do no take into acount the ''translations'' phase.
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= III - Estimation of Paramaters =
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== III - Estimation of Paramaters ==
Here we present our job on finding [[Team:Paris/Modeling/estimation_of_parameters|relevent parameters]] for our models. In particular, we are looking for parameters involved in our [[Team:Paris/Modeling/hill_approach|"Hill" functions]].
Here we present our job on finding [[Team:Paris/Modeling/estimation_of_parameters|relevent parameters]] for our models. In particular, we are looking for parameters involved in our [[Team:Paris/Modeling/hill_approach|"Hill" functions]].
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Thus, we have described the experimental approach required : [[Team:Paris/Modeling/estimation|Estimation of the parameters]].
Thus, we have described the experimental approach required : [[Team:Paris/Modeling/estimation|Estimation of the parameters]].
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= IV - Parameters & Bibliography =
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== IV - Parameters & Bibliography ==
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==Bibliography==
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* [[Team:Paris/Modeling/Bibliography|Bibliography]]
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<br>
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* [1] Shiraz Kalir, Uri Alon. Using quantitative blueprint to reprogram the dynamics of the flagella network. Cell, June 11, 2004, Vol.117, 713-720.
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* [2]Jordi Garcia-Ojalvo, Michael B. Elowitz, Steven H. Strogratz. Modeling a synthetic multicellular clock : repressilators coupled by quorum sensing. PNAS, July 27, 204, Vol. 101, no. 30.
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* [3]Nitzan Rosenfeld, Uri Alon. Response delays and the structure of transcription networks. JMB, 2003, 329, 645-654.
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* [4]Nitzan Rosenfeld, Michael B. Elowitz, Uri Alon. Negative autoregulation speeds the response times of transcription networks. JMB, 2003, 323, 785-793.
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* [5]S.Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, S. Leibler, M. G. Surette, U. Alon. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science, June 2001, Vol 292.
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==== V - Annexes ====
==== V - Annexes ====

Revision as of 14:25, 12 August 2008

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

If you want to have a look at our modeling notebook: Notebook

Presentation of our work

The different phases of our modeling work... The following presentation is not necessarly chronological, but presents the advantage of introducing our work from the simplest model to the most complicated.

I - Linear Approach

An Oscillatory Biological Model, with almost only linear relationships.

II - "Hill" Approach

That was our first approach, which we would like to study as far as possible. The estimation of parameters is mostly for this one.

We use mostly Hill functions to describe relationships between transcription factors and promoters, and do no take into acount the translations phase.

III - Estimation of Paramaters

Here we present our job on finding relevent parameters for our models. In particular, we are looking for parameters involved in our "Hill" functions.

We will need many parameters to fully describe the system according to the asumptions of the previous models. A natural way to have access to their value, after searching in the litterature, is to devise specific experiments. As a consequence of the characterization of the promoters activity, some Hill functions could be obtained.

Thus, we have described the experimental approach required : Estimation of the parameters.

IV - Parameters & Bibliography

V - Annexes

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