Team:Paris/Modeling/Implementation

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[[https://2008.igem.org/Team:Paris/Modeling/Workflow_Example Back to "Workflow on an Example"]]

We use '''Matlab''' for all implementations.

== Parameters Finder Programs ==

=== the datas ===

The experimental datas consist typically in two tables, <span style="color:#0000FF;">X_data</span> (various concentrations of the transcription factor) and <span style="color:#0000FF;">Y_data</span> (corresponding output values). 

* controlling X_data : thanks to the prior characterization of the inductible promoters that control the transcription factor concentrations, we can deduce from the <span style="color:#0000FF;">Inv_f1.m</span> and <span style="color:#0000FF;">Inv_f2.m</span> functions the necessary concentrations of ''aTc'' and ''arabinose'' to introduce in the medium to get the wanted concentrations of transcription factor.

* getting Y_data : the linear <span style="color:#0000FF;">conversion</span> between the fluorescence of GFP at maturation and its concentration gives us directly the expected datas.

=== Parameters Finder for our Example ===

We just write here the annoted program find_FP that is used to estimate, for instance, the parameters in :
* <span style="color:#0000FF;">&#131;5( [''FlhDC''], 0 ) = ''&beta;<sub>24</sub> * &#131;<sub>hill</sub>''( [''FlhDC''], ''K<sub>2</sub>'', ''n<sub>2</sub>'' )</span> and 
* <span style="color:#0000FF;">&#131;5( 0, [''FliA''] ) = ''&beta;<sub>25</sub> * &#131;<sub>hill</sub>''( [''FliA''], ''K<sub>8</sub>'', ''n<sub>8</sub>'' )</span>