Team:Paris/Modeling/Workflow Example

From 2008.igem.org

(Difference between revisions)
(→Generic Workflow on an Example)
 
(140 intermediate revisions not shown)
Line 1: Line 1:
-
= Generic Workflow on an Example =
+
{{Paris/Menu}}
 +
{{Paris/Header|Characterization Approach : Application of our Generic Workflow - an Example}}
 +
{{Paris/Section_contents_characterization}}
-
Here, we will explain the generic protocole that leads to the caracterisation of one of the steps of the system. The choosen example is '''the EXPRESSION of the PROMOTER pFliL in function of the TRANSCRIPTION FACTORS FlhDC and FliA'''.
+
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>
-
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 action ?
+
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>
-
 
+
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)'''.
-
{|border="0" style="text-align: right"
+
<br>
-
|<center> Steps </center>
+
<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> Corresponding Hypothesis and Methods </center>
+
<br>
 +
<center>
 +
{|border="0" style="text-align: center" cellspacing="-1"
 +
|'''Modelisation'''
 +
|'''Experiments'''
|-
|-
-
| First, we consider the complexations ''FlhDC><pFliL'' and ''FlhDC><pFliL'' :
+
|<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>
-
|[[Team:Paris/Modeling/Specific_Hypothesis#Hexamere|''FlhD<sub>4</sub>C<sub>2</sub>'' &rarr; ''FlhDC'']] <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>
-
[[Team:Paris/Modeling/General_Hypothesis#Complexations#Elementary_Reaction|Quasi Steady-State]] <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>
-
[[Team:Paris/Modeling/General_Hypothesis#Complexations#Hill_Type|"Hill Type" complexation]] <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#All_Algorithm"><img src="https://static.igem.org/mediawiki/2008/3/31/Goal.jpg" width=480></a></html>
-
|[[Image:complexation.jpg]]
+
|<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_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/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>
-
| Then, we consider the resulting activation of ''pFliL'' :
+
<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>
-
|[[Team:Paris/Modeling/General_Hypothesis#Transduction_Rate|Transduction Rate &beta;]] <br>
+
<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>
-
[[Team:Paris/Modeling/Specific_Hypothesis#SUM|"Sum Logical Gate"]] <br>
+
-
|-
+
-
|[[Image:activation]]
+
-
|
+
-
|-
+
-
|
+
-
|
+
-
|-
+
-
|
+
-
|
+
-
|-
+
-
|
+
-
|
+
|}
|}
 +
</center>
 +
 +
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">


Retrieved from "http://2008.igem.org/Team:Paris/Modeling/Workflow_Example"