Team:Paris/Modeling/Workflow Example

From 2008.igem.org

(Difference between revisions)
 
(41 intermediate revisions not shown)
Line 1: Line 1:
{{Paris/Menu}}
{{Paris/Menu}}
-
{{Paris/Header|Generic Workflow on an Example}}
+
{{Paris/Header|Characterization Approach : Application of our Generic Workflow - an Example}}
 +
{{Paris/Section_contents_characterization}}
-
[[Team:Paris/Modeling/Characterization_Approach|return to the "Presentation"]]
+
Here, we explain the generic protocol that leads to modeling "by characterization", throught one of the parts of our system. The chosen example is '''the activity of the promoter ''pFliL'' ''' (that leads, in the [[Team:Paris/Analysis#Oscillations|core system]], to the production of the '''Fluorescent Protein FP1''') '''in function of the transcription factors ''FlhDC'' and ''FliA'' '''.<br>
-
 
+
-
Here, we will explain the generic protocol that leads to the characterisation of one of the steps of our system. The choosen example is '''the ACTIVITY of the PROMOTER pFliL''' (that leads to the production of the '''Fluorescent Protein FP1''') '''in function of the TRANSCRIPTION FACTORS FlhDC and FliA'''.
+
We know that ''the hexamere FlhD<sub>4</sub>C<sub>2</sub>'' and the protein ''FliA'' act both on the promoter ''pFliL'' as inducers... how do we evaluate this phenomenon? <br>
We know that ''the hexamere FlhD<sub>4</sub>C<sub>2</sub>'' and the protein ''FliA'' act both on the promoter ''pFliL'' as inducers... how do we evaluate this phenomenon? <br>
-
Starting from [[Team:Paris/Modeling/Molecular_Reactions|molecular reactions]] '''(1)''', we develop a [[Team:Paris/Modeling/FromMolReactToNLOde|model of our system]] '''(2)''', and then we identify the parameters '''(3)''' that needs to be estimated. Essentially, it amounts to estimate [[Team:Paris/Modeling/Protocol_Of_Characterisation|Promoters Activities as functions of their Transcription Factors]]. To do so, we propose [[Team:Paris/Modeling/Protocol_Of_Characterisation|constructs]] '''(4)''', [[Team:Paris/Modeling/Protocol_Of_Characterisation|protocols]] '''(5)''' and [[Team:Paris/Modeling/Implementation|programs]] '''(6)'''.
+
As it is illustrated below; starting from ''molecular reactions'' '''(1)''', we develop a ''model of our system'' '''(2)''', and then we identify the ''parameters'' '''(3)''' that need to be estimated. Essentially, it amounts to estimate ''Promoters Activities as functions of their Transcription Factors''. To do so, we propose ''constructs'' '''(4)''', ''protocols'' '''(5)''' and ''programs'' '''(6)'''.
-
 
+
<br>
<br>
-
 
+
<center><span style="color: red; font-weight: bold; font-size: 28">CLICK on the images below for further information on each step!</span></center>  
-
<center> ''You can click on the images to get further informations on the represented step''</center>  
+
-
 
+
<br>
<br>
-
 
<center>
<center>
{|border="0" style="text-align: center" cellspacing="-1"
{|border="0" style="text-align: center" cellspacing="-1"
Line 21: Line 16:
|<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Molecular_Reactions"><img src="https://static.igem.org/mediawiki/2008/e/e3/Molecular_Reactions.jpg" width=480></a></html><br>
|<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Molecular_Reactions"><img src="https://static.igem.org/mediawiki/2008/e/e3/Molecular_Reactions.jpg" width=480></a></html><br>
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/FromMolReactToNLOde"><img src="https://static.igem.org/mediawiki/2008/b/b1/HypothesisModel.jpg" width=480></a></html><br>
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/FromMolReactToNLOde"><img src="https://static.igem.org/mediawiki/2008/b/b1/HypothesisModel.jpg" width=480></a></html><br>
-
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Full_System_Of_Ode"><img src="https://static.igem.org/mediawiki/2008/8/85/TemporalVariation.jpg" width=480></a></html><br>
+
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/FromMolReactToNLOde#Mathematical_Interpretation_and_Simulation_of_the_Molecular_Reactions"><img src="https://static.igem.org/mediawiki/2008/8/85/TemporalVariation.jpg" width=480></a></html><br>
-
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/FromMolReactToNLOde"><img src="https://static.igem.org/mediawiki/2008/4/40/RQSS.jpg" width=240></a></html><html><a href = "https://2008.igem.org/Team:Paris/Modeling/Implementation"><img src="https://static.igem.org/mediawiki/2008/b/b4/Programs.jpg" width=240></a></html> <br>
+
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/FromMolReactToNLOde#Mathematical_Interpretation_and_Simulation_of_the_Molecular_Reactions"><img src="https://static.igem.org/mediawiki/2008/4/40/RQSS.jpg" width=240></a></html><html><a href = "https://2008.igem.org/Team:Paris/Modeling/Implementation#Parameters_Finder_Programs"><img src="https://static.igem.org/mediawiki/2008/b/b4/Programs.jpg" width=240></a></html> <br>
-
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Implementation"><img src="https://static.igem.org/mediawiki/2008/3/31/Goal.jpg" width=480></a></html>
+
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Implementation#All_Algorithm"><img src="https://static.igem.org/mediawiki/2008/3/31/Goal.jpg" width=480></a></html>
-
|<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Protocol_Of_Characterisation"><img src="https://static.igem.org/mediawiki/2008/f/fd/Principles.jpg" width=410></a></html><br>
+
|<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Protocol_Of_Characterization"><img src="https://static.igem.org/mediawiki/2008/f/fd/Principles.jpg" width=410></a></html><br>
-
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Protocol_Of_Characterisation"><img src="https://static.igem.org/mediawiki/2008/5/52/Plasmid.jpg" width=410></a></html><br>
+
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Protocol_Of_Characterization#II-Plasmid_for_promoter_characterization"><img src="https://static.igem.org/mediawiki/2008/5/52/Plasmid.jpg" width=410></a></html><br>
-
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/FromMolReactToNLOde"><img src="https://static.igem.org/mediawiki/2008/7/78/HypothesisCharact.jpg" width=410></a></html><br>
+
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Protocol_Of_Characterization#Specific_Assumptions_for_the_Experiments"><img src="https://static.igem.org/mediawiki/2008/7/78/HypothesisCharact.jpg" width=410></a></html><br>
-
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Implementation"><img src="https://static.igem.org/mediawiki/2008/7/78/Graph.jpg" width=410></a></html><br>
+
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Implementation#Parameters_Finder_Programs"><img src="https://static.igem.org/mediawiki/2008/7/78/Graph.jpg" width=410></a></html><br>
-
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Implementation"><img src="https://static.igem.org/mediawiki/2008/8/83/FullSystem.jpg" width=410></a></html>
+
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Implementation#All_Algorithms"><img src="https://static.igem.org/mediawiki/2008/8/83/FullSystem.jpg" width=410></a></html>
|}
|}
</center>
</center>
-
Once we get every parameters for every functions involved in our Full System, we have got a "Modular Virtual Lab" of our System that aims to be ''' ''predictive'' '''.
+
By estimating all parameters of every function involved in our Full System, we achieve a "Modular Virtual Lab" of our System with potential ''predictive'' capacity.
 +
 
 +
<br>
 +
 
 +
<div style="text-align: center">
 +
{{Paris/Toggle|Details on the Steps|Team:Paris/Modeling/Rubriques|250px}}
 +
</div>
 +
 
 +
<br>
 +
 
 +
<center>
 +
[[Team:Paris/Modeling/Characterization_Approach| <Back - to the "Presentation" ]]|[[Team:Paris/Modeling/Characterization_Approach_Conclu| Next - to the "Conclusion"> ]]
 +
</center>
 +
 
 +
{{Paris/Navig|Team:Paris/Modeling/Workflow_Example}}

Latest revision as of 05:16, 30 October 2008

Characterization Approach : Application of our Generic Workflow - an Example


Here, we explain the generic protocol that leads to modeling "by characterization", throught one of the parts of our system. The chosen example is the activity of the promoter pFliL (that leads, in the core system, to the production of the Fluorescent Protein FP1) in function of the transcription factors FlhDC and FliA .
We know that the hexamere FlhD4C2 and the protein FliA act both on the promoter pFliL as inducers... how do we evaluate this phenomenon?
As it is illustrated below; starting from molecular reactions (1), we develop a model of our system (2), and then we identify the parameters (3) that need to be estimated. Essentially, it amounts to estimate Promoters Activities as functions of their Transcription Factors. To do so, we propose constructs (4), protocols (5) and programs (6).

CLICK on the images below for further information on each step!


Modelisation Experiments








By estimating all parameters of every function involved in our Full System, we achieve a "Modular Virtual Lab" of our System with potential predictive capacity.



<Back - to the "Presentation" | Next - to the "Conclusion">