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2024-03-29T13:56:33Z
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http://2008.igem.org/Team:Paris/Modeling/Workflow_Example
Team:Paris/Modeling/Workflow Example
2008-10-30T05:16:21Z
<p>Hugo: </p>
<hr />
<div>{{Paris/Menu}}<br />
{{Paris/Header|Characterization Approach : Application of our Generic Workflow - an Example}}<br />
{{Paris/Section_contents_characterization}}<br />
<br />
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><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><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)'''.<br />
<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> <br />
<br><br />
<center><br />
{|border="0" style="text-align: center" cellspacing="-1"<br />
|'''Modelisation'''<br />
|'''Experiments'''<br />
|-<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><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><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><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><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><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><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><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><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><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><br />
|}<br />
</center><br />
<br />
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 />
<br />
<br><br />
<br />
<div style="text-align: center"><br />
{{Paris/Toggle|Details on the Steps|Team:Paris/Modeling/Rubriques|250px}} <br />
</div><br />
<br />
<br><br />
<br />
<center><br />
[[Team:Paris/Modeling/Characterization_Approach| <Back - to the "Presentation" ]]|[[Team:Paris/Modeling/Characterization_Approach_Conclu| Next - to the "Conclusion"> ]]<br />
</center><br />
<br />
{{Paris/Navig|Team:Paris/Modeling/Workflow_Example}}</div>
Hugo
http://2008.igem.org/Team:Paris/Modeling/Workflow_Example
Team:Paris/Modeling/Workflow Example
2008-10-30T05:14:58Z
<p>Hugo: </p>
<hr />
<div>{{Paris/Menu}}<br />
{{Paris/Header|Characterization Approach : Application of our Generic Workflow - an Example}}<br />
{{Paris/Section_contents_characterization}}<br />
<br />
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><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><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)'''.<br />
<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> <br />
<br><br />
<center><br />
{|border="0" style="text-align: center" cellspacing="-1"<br />
|'''Modelisation'''<br />
|'''Experiments'''<br />
|-<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><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><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><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><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><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><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><br />
<html><a href = "https://2008.igem.org/Team:Paris/Modeling/Protocol_Of_Characterization"><img src="https://static.igem.org/mediawiki/2008/7/78/HypothesisCharact.jpg" width=410></a></html><br><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><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><br />
|}<br />
</center><br />
<br />
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 />
<br />
<br><br />
<br />
<div style="text-align: center"><br />
{{Paris/Toggle|Details on the Steps|Team:Paris/Modeling/Rubriques|250px}} <br />
</div><br />
<br />
<br><br />
<br />
<center><br />
[[Team:Paris/Modeling/Characterization_Approach| <Back - to the "Presentation" ]]|[[Team:Paris/Modeling/Characterization_Approach_Conclu| Next - to the "Conclusion"> ]]<br />
</center><br />
<br />
{{Paris/Navig|Team:Paris/Modeling/Workflow_Example}}</div>
Hugo
http://2008.igem.org/Team:Paris/Modeling/Characterization_Approach_Conclu
Team:Paris/Modeling/Characterization Approach Conclu
2008-10-30T05:13:02Z
<p>Hugo: </p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
{{Paris/Header|Characterization Approach : Discussions & Conclusion}}<br />
<br />
The characterisation approach is now ready and awaits further bench work to achieve the plasmid cloning.<br />
<br />
Significantly, we developed a complete rational workflow for parameter measurements and model building, that can be applied generically for the benefit of the synthetic biology community where such a modular and predictive framework is greatly needed.<br />
<br />
<br><br />
<br />
<center><br />
[[Team:Paris/Modeling/Workflow_Example| <Back - to "Workflow on an Example"]] |<br />
</center><br />
<br />
<br><br />
<br />
{{Paris/Navig|Team:Paris/Modeling/Workflow_Example}}</div>
Hugo
http://2008.igem.org/Team:Paris/Modeling/Characterization_Approach_Conclu
Team:Paris/Modeling/Characterization Approach Conclu
2008-10-30T05:12:47Z
<p>Hugo: </p>
<hr />
<div>{{Paris/Menu}}<br />
<br />
{{Paris/Header|Characterization Approach : Discussions & Conclusion}}<br />
<br />
The characterisation approach is now ready and awaits further bench work to achieve the plasmid cloning.<br />
<br />
Significantly, we developed a complete rational workflow for parameter measurements and model building, that can be applied generically for the benefit of the synthetic biology community where such a modular and predictive framework is greatly needed.<br />
<br />
<center><br />
[[Team:Paris/Modeling/Workflow_Example| <Back - to "Workflow on an Example"]] |<br />
</center><br />
<br />
<br><br />
<br />
{{Paris/Navig|Team:Paris/Modeling/Workflow_Example}}</div>
Hugo
http://2008.igem.org/Team:Paris/Modeling/Others_prog
Team:Paris/Modeling/Others prog
2008-10-30T05:04:42Z
<p>Hugo: /* Global */</p>
<hr />
<div><html><br />
<style type="text/css"><br />
<br />
pre {font-size: 1.2em}<br />
span.keyword {color: #0000FF}<br />
span.comment {color: #228B22}<br />
span.string {color: #A020F0}<br />
span.untermstring {color: #B20000}<br />
span.syscmd {color: #B28C00}<br />
}<br />
<br />
</style><br />
</html><br />
<br />
<div style="text-align: left"><br />
== complexes ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> complexes = complexes(x,y,K,n)<br />
<span class="comment">% amount of complexes n*x + y = x_-_y in function of x, y<br />
</span> <br />
<span class="comment">% x, y = initial amounts of binding molecules<br />
</span><span class="comment">% K = dissociation constant<br />
</span><span class="comment">% n = stoechiometric coefficient of x<br />
</span> <br />
syms <span class="string">z;</span><span class="comment"> % to treat z as a symbolic variable<br />
</span>Eqn = ( ( x - n*z )^n )*( y - z ) - K*z;<span class="comment"> % to define the equation in whose<br />
</span> <span class="comment"> % the amount of complexes is a root <br />
</span> <br />
S = eval(solve( Eqn, <span class="string">'z'</span> ));<span class="comment"> % the vector of the roots<br />
</span> <br />
Index = find ((0 < S) & (n*S < x) & (S < y) & (imag(S) == 0));<span class="comment"> % determine <br />
</span> <span class="comment"> % which<br />
</span> <span class="comment"> % root is <br />
</span> <span class="comment"> % acceptable<br />
</span> <br />
complexes = S(Index(1));<span class="comment"> % the result<br />
</span> <br />
<span class="keyword">end</span><br />
</pre></html><br />
<br />
== hill ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> compl = hill(x,K,n)<br />
<span class="comment">% complexation nx + Y = x_-_Y when x is in large excess :<br />
</span><span class="comment">% gives the ratio (x_-_Y)/(Ytotal) in function of x<br />
</span> <br />
<span class="comment">% x = molecule that binds to Y<br />
</span><span class="comment">% K^n = dissociation constant<br />
</span><span class="comment">% n = stoechiometric coefficient of x ; also known as 'cooperativity'<br />
</span> <br />
compl = x^n/(K^n + x^n);<br />
<br />
<span class="keyword">end</span><br />
</pre></html><br />
<br />
== Global ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> labo=Core_Sytem_Simulation (t, init, prom1, prom2, retro)<br />
<span class="comment">% Simulation of our Core_System<br />
</span> <br />
<span class="comment">% prom1 = 'pTet' or 'pFlhDC'<br />
</span><span class="comment">% prom2 = 'pFlgA' or 'pFlgB'<br />
</span><span class="comment">% retro = 'EnvZ' or 'OmpR' or quantity of aTc<br />
</span> <br />
<span class="comment">% t = discret time scale<br />
</span><span class="comment">% init = vector of the initial state<br />
</span><span class="comment">% [FlhDC;<br />
</span><span class="comment">% FliA;<br />
</span><span class="comment">% FP1;<br />
</span><span class="comment">% FP2;<br />
</span><span class="comment">% FP3;<br />
</span><span class="comment">% TetR / OmpR / EnvZ] regards to the studied version<br />
</span> <br />
<span class="keyword">global</span> gamma beta16 K13 n13 K12 n12 K15 n15 beta17 K6 n6 ...<br />
beta22 beta18 K1 n1 beta23 K7 n7 beta24 K2 n2 ...<br />
beta25 K8 n8 gamma37 beta26 K3 n3 beta27 K9 n9 ...<br />
gamma38 beta28 K4 n4 beta29 K10 n10 beta30 K5 n5 ...<br />
beta31 K11 n11 gamma39 EnvZ_b OmpR_b K14 n14; <br />
<span class="comment">% A program must load all parameters !<br />
</span> <br />
<span class="keyword">if</span> prom2 == <span class="string">'pFlgA'</span><br />
F = @f6<br />
<span class="keyword">elseif</span> prom2 == <span class="string">'pFlgA'</span><br />
F = @f7<br />
<span class="keyword">end</span><br />
<span class="keyword">else</span> error(<span class="string">'Wrong promoter for FP2 '</span>)<br />
<span class="keyword">end</span><br />
<br />
<span class="keyword">if</span> prom1 == <span class="string">'pTet'</span><br />
<span class="keyword">try</span> aTc = eval(retro)<br />
<span class="keyword">catch</span> error(<span class="string">'Wrong aTc Value'</span>)<br />
<span class="keyword">end</span><br />
<br />
<span class="keyword">function</span> ydot = deriv(t,y)<span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pTet : y(6) = TetR ; retro = aTc<br />
</span> ydot = [f1(y(6), aTc);<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
<span class="keyword">elseif</span> prom1 == <span class="string">'pFlhDC'</span><br />
<span class="keyword">if</span> retro == <span class="string">'OmpR'</span><br />
<span class="keyword">function</span> ydot = deriv(t,y) <span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pFlhDC : y(6) = OmpR<br />
</span> ydot = [f3(y(2), y(6));<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
<span class="keyword">elseif</span> retro == <span class="string">'EnvZ'</span><br />
<span class="keyword">function</span> ydot = deriv(t,y) <span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pFlhDC : y(6) = EnvZ<br />
</span> ydot = [f3bis(y(6), y(2));<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
<span class="keyword">else</span><br />
error(<span class="string">'gene for negative feed-back'</span>)<br />
<span class="keyword">end</span><br />
<span class="keyword">else</span><br />
error(<span class="string">'Wrong promoter for flhDC'</span>)<br />
<span class="keyword">end</span><br />
<span class="keyword">end</span><br />
<br />
[t,labo]=ode45(deriv,t,init);<br />
<br />
<span class="comment">% The 'full modularity' of this Approach allow other variations, <br />
</span><span class="comment">% like changing the place of the negative feed-back<br />
</span><span class="comment">% (changing f8 by f7, f6, f5)...</span><br />
</pre></html><br />
<br />
</div></div>
Hugo
http://2008.igem.org/Team:Paris/Modeling/Others_prog
Team:Paris/Modeling/Others prog
2008-10-30T05:03:52Z
<p>Hugo: /* Global */</p>
<hr />
<div><html><br />
<style type="text/css"><br />
<br />
pre {font-size: 1.2em}<br />
span.keyword {color: #0000FF}<br />
span.comment {color: #228B22}<br />
span.string {color: #A020F0}<br />
span.untermstring {color: #B20000}<br />
span.syscmd {color: #B28C00}<br />
}<br />
<br />
</style><br />
</html><br />
<br />
<div style="text-align: left"><br />
== complexes ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> complexes = complexes(x,y,K,n)<br />
<span class="comment">% amount of complexes n*x + y = x_-_y in function of x, y<br />
</span> <br />
<span class="comment">% x, y = initial amounts of binding molecules<br />
</span><span class="comment">% K = dissociation constant<br />
</span><span class="comment">% n = stoechiometric coefficient of x<br />
</span> <br />
syms <span class="string">z;</span><span class="comment"> % to treat z as a symbolic variable<br />
</span>Eqn = ( ( x - n*z )^n )*( y - z ) - K*z;<span class="comment"> % to define the equation in whose<br />
</span> <span class="comment"> % the amount of complexes is a root <br />
</span> <br />
S = eval(solve( Eqn, <span class="string">'z'</span> ));<span class="comment"> % the vector of the roots<br />
</span> <br />
Index = find ((0 < S) & (n*S < x) & (S < y) & (imag(S) == 0));<span class="comment"> % determine <br />
</span> <span class="comment"> % which<br />
</span> <span class="comment"> % root is <br />
</span> <span class="comment"> % acceptable<br />
</span> <br />
complexes = S(Index(1));<span class="comment"> % the result<br />
</span> <br />
<span class="keyword">end</span><br />
</pre></html><br />
<br />
== hill ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> compl = hill(x,K,n)<br />
<span class="comment">% complexation nx + Y = x_-_Y when x is in large excess :<br />
</span><span class="comment">% gives the ratio (x_-_Y)/(Ytotal) in function of x<br />
</span> <br />
<span class="comment">% x = molecule that binds to Y<br />
</span><span class="comment">% K^n = dissociation constant<br />
</span><span class="comment">% n = stoechiometric coefficient of x ; also known as 'cooperativity'<br />
</span> <br />
compl = x^n/(K^n + x^n);<br />
<br />
<span class="keyword">end</span><br />
</pre></html><br />
<br />
== Global ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> labo=Core_Sytem_Simulation (t, init, prom1, prom2, retro)<br />
<span class="comment">% Simulation of our Core_System<br />
</span> <br />
<span class="comment">% prom1 = 'pTet' or 'pFlhDC'<br />
</span><span class="comment">% prom2 = 'pFlgA' or 'pFlgB'<br />
</span><span class="comment">% retro = 'EnvZ' or 'OmpR' or quantity of aTc<br />
</span> <br />
<span class="comment">% t = discret time scale<br />
</span><span class="comment">% init = vector of the initial state<br />
</span><span class="comment">% [FlhDC;<br />
</span><span class="comment">% FliA;<br />
</span><span class="comment">% FP1;<br />
</span><span class="comment">% FP2;<br />
</span><span class="comment">% FP3;<br />
</span><span class="comment">% TetR / OmpR / EnvZ] regards to the studied version<br />
</span> <br />
<span class="keyword">global</span> gamma beta16 K13 n13 K12 n12 K15 n15 beta17 K6 n6 ...<br />
beta22 beta18 K1 n1 beta23 K7 n7 beta24 K2 n2 ...<br />
beta25 K8 n8 gamma37 beta26 K3 n3 beta27 K9 n9 ...<br />
gamma38 beta28 K4 n4 beta29 K10 n10 beta30 K5 n5 ...<br />
beta31 K11 n11 gamma39 EnvZ_b OmpR_b K14 n14; <br />
<span class="comment">% A program must load all parameters !<br />
</span> <br />
<span class="keyword">if</span> prom2 == <span class="string">'pFlgA'</span><br />
F = @f6<br />
<span class="keyword">elseif</span> prom2 == <span class="string">'pFlgA'</span><br />
F = @f7<br />
<span class="keyword">end</span><br />
<span class="keyword">else</span> error(<span class="string">'Wrong promoter for FP2 '</span>)<br />
<span class="keyword">end</span><br />
<br />
if prom1 == <span class="string">'pTet'</span><br />
<span class="keyword">try</span> aTc = eval(retro)<br />
<span class="keyword">catch</span> error(<span class="string">'Wrong aTc Value'</span>)<br />
<span class="keyword">end</span><br />
<br />
<span class="keyword">function</span> ydot = deriv(t,y)<span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pTet : y(6) = TetR ; retro = aTc<br />
</span> ydot = [f1(y(6), aTc);<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
<span class="keyword">elseif</span> prom1 == <span class="string">'pFlhDC'</span><br />
<span class="keyword">if</span> retro == <span class="string">'OmpR'</span><br />
<span class="keyword">function</span> ydot = deriv(t,y) <span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pFlhDC : y(6) = OmpR<br />
</span> ydot = [f3(y(2), y(6));<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
<span class="keyword">elseif</span> retro == <span class="string">'EnvZ'</span><br />
<span class="keyword">function</span> ydot = deriv(t,y) <span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pFlhDC : y(6) = EnvZ<br />
</span> ydot = [f3bis(y(6), y(2));<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
<span class="keyword">else</span><br />
error(<span class="string">'gene for negative feed-back'</span>)<br />
<span class="keyword">end</span><br />
<span class="keyword">else</span><br />
error(<span class="string">'Wrong promoter for flhDC'</span>)<br />
<span class="keyword">end</span><br />
<span class="keyword">end</span><br />
<br />
[t,labo]=ode45(deriv,t,init);<br />
<br />
<span class="comment">% The 'full modularity' of this Approach allow other variations, <br />
</span><span class="comment">% like changing the place of the negative feed-back<br />
</span><span class="comment">% (changing f8 by f7, f6, f5)...</span><br />
</pre></html><br />
<br />
</div></div>
Hugo
http://2008.igem.org/Team:Paris/Modeling/Others_prog
Team:Paris/Modeling/Others prog
2008-10-30T05:02:49Z
<p>Hugo: /* Global */</p>
<hr />
<div><html><br />
<style type="text/css"><br />
<br />
pre {font-size: 1.2em}<br />
span.keyword {color: #0000FF}<br />
span.comment {color: #228B22}<br />
span.string {color: #A020F0}<br />
span.untermstring {color: #B20000}<br />
span.syscmd {color: #B28C00}<br />
}<br />
<br />
</style><br />
</html><br />
<br />
<div style="text-align: left"><br />
== complexes ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> complexes = complexes(x,y,K,n)<br />
<span class="comment">% amount of complexes n*x + y = x_-_y in function of x, y<br />
</span> <br />
<span class="comment">% x, y = initial amounts of binding molecules<br />
</span><span class="comment">% K = dissociation constant<br />
</span><span class="comment">% n = stoechiometric coefficient of x<br />
</span> <br />
syms <span class="string">z;</span><span class="comment"> % to treat z as a symbolic variable<br />
</span>Eqn = ( ( x - n*z )^n )*( y - z ) - K*z;<span class="comment"> % to define the equation in whose<br />
</span> <span class="comment"> % the amount of complexes is a root <br />
</span> <br />
S = eval(solve( Eqn, <span class="string">'z'</span> ));<span class="comment"> % the vector of the roots<br />
</span> <br />
Index = find ((0 < S) & (n*S < x) & (S < y) & (imag(S) == 0));<span class="comment"> % determine <br />
</span> <span class="comment"> % which<br />
</span> <span class="comment"> % root is <br />
</span> <span class="comment"> % acceptable<br />
</span> <br />
complexes = S(Index(1));<span class="comment"> % the result<br />
</span> <br />
<span class="keyword">end</span><br />
</pre></html><br />
<br />
== hill ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> compl = hill(x,K,n)<br />
<span class="comment">% complexation nx + Y = x_-_Y when x is in large excess :<br />
</span><span class="comment">% gives the ratio (x_-_Y)/(Ytotal) in function of x<br />
</span> <br />
<span class="comment">% x = molecule that binds to Y<br />
</span><span class="comment">% K^n = dissociation constant<br />
</span><span class="comment">% n = stoechiometric coefficient of x ; also known as 'cooperativity'<br />
</span> <br />
compl = x^n/(K^n + x^n);<br />
<br />
<span class="keyword">end</span><br />
</pre></html><br />
<br />
== Global ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> labo=Core_Sytem_Simulation (t, init, prom1, prom2, retro)<br />
<span class="comment">% Simulation of our Core_System<br />
</span> <br />
<span class="comment">% prom1 = 'pTet' or 'pFlhDC'<br />
</span><span class="comment">% prom2 = 'pFlgA' or 'pFlgB'<br />
</span><span class="comment">% retro = 'EnvZ' or 'OmpR' or quantity of aTc<br />
</span> <br />
<span class="comment">% t = discret time scale<br />
</span><span class="comment">% init = vector of the initial state<br />
</span><span class="comment">% [FlhDC;<br />
</span><span class="comment">% FliA;<br />
</span><span class="comment">% FP1;<br />
</span><span class="comment">% FP2;<br />
</span><span class="comment">% FP3;<br />
</span><span class="comment">% TetR / OmpR / EnvZ] regards to the studied version<br />
</span> <br />
<span class="keyword">global</span> gamma beta16 K13 n13 K12 n12 K15 n15 beta17 K6 n6 ...<br />
beta22 beta18 K1 n1 beta23 K7 n7 beta24 K2 n2 ...<br />
beta25 K8 n8 gamma37 beta26 K3 n3 beta27 K9 n9 ...<br />
gamma38 beta28 K4 n4 beta29 K10 n10 beta30 K5 n5 ...<br />
beta31 K11 n11 gamma39 EnvZ_b OmpR_b K14 n14; <br />
<span class="comment">% A program must load all parameters !<br />
</span> <br />
if prom2 == <span class="string">'pFlgA'</span><br />
F = @f6<br />
elseif prom2 == <span class="string">'pFlgA'</span><br />
F = @f7<br />
<span class="keyword">end</span><br />
else error(<span class="string">'Wrong promoter for FP2 '</span>)<br />
<span class="keyword">end</span><br />
<br />
if prom1 == <span class="string">'pTet'</span><br />
<span class="keyword">try</span> aTc = eval(retro)<br />
<span class="keyword">catch</span> error(<span class="string">'Wrong aTc Value'</span>)<br />
<span class="keyword">end</span><br />
<br />
<span class="keyword">function</span> ydot = deriv(t,y)<span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pTet : y(6) = TetR ; retro = aTc<br />
</span> ydot = [f1(y(6), aTc);<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
<span class="keyword">elseif</span> prom1 == <span class="string">'pFlhDC'</span><br />
<span class="keyword">if</span> retro == <span class="string">'OmpR'</span><br />
<span class="keyword">function</span> ydot = deriv(t,y) <span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pFlhDC : y(6) = OmpR<br />
</span> ydot = [f3(y(2), y(6));<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
<span class="keyword">elseif</span> retro == <span class="string">'EnvZ'</span><br />
<span class="keyword">function</span> ydot = deriv(t,y) <span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pFlhDC : y(6) = EnvZ<br />
</span> ydot = [f3bis(y(6), y(2));<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
<span class="keyword">else</span><br />
error(<span class="string">'gene for negative feed-back'</span>)<br />
<span class="keyword">end</span><br />
<span class="keyword">else</span><br />
error(<span class="string">'Wrong promoter for flhDC'</span>)<br />
<span class="keyword">end</span><br />
<span class="keyword">end</span><br />
<br />
[t,labo]=ode45(deriv,t,init);<br />
<br />
<span class="comment">% The 'full modularity' of this Approach allow other variations, <br />
</span><span class="comment">% like changing the place of the negative feed-back<br />
</span><span class="comment">% (changing f8 by f7, f6, f5)...</span><br />
</pre></html><br />
<br />
</div></div>
Hugo
http://2008.igem.org/Team:Paris/Modeling/Others_prog
Team:Paris/Modeling/Others prog
2008-10-30T04:57:45Z
<p>Hugo: /* Global */</p>
<hr />
<div><html><br />
<style type="text/css"><br />
<br />
pre {font-size: 1.2em}<br />
span.keyword {color: #0000FF}<br />
span.comment {color: #228B22}<br />
span.string {color: #A020F0}<br />
span.untermstring {color: #B20000}<br />
span.syscmd {color: #B28C00}<br />
}<br />
<br />
</style><br />
</html><br />
<br />
<div style="text-align: left"><br />
== complexes ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> complexes = complexes(x,y,K,n)<br />
<span class="comment">% amount of complexes n*x + y = x_-_y in function of x, y<br />
</span> <br />
<span class="comment">% x, y = initial amounts of binding molecules<br />
</span><span class="comment">% K = dissociation constant<br />
</span><span class="comment">% n = stoechiometric coefficient of x<br />
</span> <br />
syms <span class="string">z;</span><span class="comment"> % to treat z as a symbolic variable<br />
</span>Eqn = ( ( x - n*z )^n )*( y - z ) - K*z;<span class="comment"> % to define the equation in whose<br />
</span> <span class="comment"> % the amount of complexes is a root <br />
</span> <br />
S = eval(solve( Eqn, <span class="string">'z'</span> ));<span class="comment"> % the vector of the roots<br />
</span> <br />
Index = find ((0 < S) & (n*S < x) & (S < y) & (imag(S) == 0));<span class="comment"> % determine <br />
</span> <span class="comment"> % which<br />
</span> <span class="comment"> % root is <br />
</span> <span class="comment"> % acceptable<br />
</span> <br />
complexes = S(Index(1));<span class="comment"> % the result<br />
</span> <br />
<span class="keyword">end</span><br />
</pre></html><br />
<br />
== hill ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> compl = hill(x,K,n)<br />
<span class="comment">% complexation nx + Y = x_-_Y when x is in large excess :<br />
</span><span class="comment">% gives the ratio (x_-_Y)/(Ytotal) in function of x<br />
</span> <br />
<span class="comment">% x = molecule that binds to Y<br />
</span><span class="comment">% K^n = dissociation constant<br />
</span><span class="comment">% n = stoechiometric coefficient of x ; also known as 'cooperativity'<br />
</span> <br />
compl = x^n/(K^n + x^n);<br />
<br />
<span class="keyword">end</span><br />
</pre></html><br />
<br />
== Global ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> labo=Core_Sytem_Simulation (t, init, prom1, prom2, retro)<br />
<span class="comment">% Simulation of our Core_System<br />
</span> <br />
<span class="comment">% prom1 = 'pTet' or 'pFlhDC'<br />
</span><span class="comment">% prom2 = 'pFlgA' or 'pFlgB'<br />
</span><span class="comment">% retro = 'EnvZ' or 'OmpR' or quantity of aTc<br />
</span> <br />
<span class="comment">% t = discret time scale<br />
</span><span class="comment">% init = vector of the initial state<br />
</span><span class="comment">% [FlhDC;<br />
</span><span class="comment">% FliA;<br />
</span><span class="comment">% FP1;<br />
</span><span class="comment">% FP2;<br />
</span><span class="comment">% FP3;<br />
</span><span class="comment">% TetR / OmpR / EnvZ] regards to the studied version<br />
</span> <br />
<span class="keyword">global</span> gamma beta16 K13 n13 K12 n12 K15 n15 beta17 K6 n6 ...<br />
beta22 beta18 K1 n1 beta23 K7 n7 beta24 K2 n2 ...<br />
beta25 K8 n8 gamma37 beta26 K3 n3 beta27 K9 n9 ...<br />
gamma38 beta28 K4 n4 beta29 K10 n10 beta30 K5 n5 ...<br />
beta31 K11 n11 gamma39 EnvZ_b OmpR_b K14 n14; <br />
<span class="comment">% A program must load all parameters !<br />
</span> <br />
if prom2 == <span class="string">'pFlgA'</span><br />
F = @f6<br />
elseif prom2 == <span class="string">'pFlgA'</span><br />
F = @f7<br />
<span class="keyword">end</span><br />
else error(<span class="string">'Wrong promoter <span class="keyword">for</span> FP2<span class="string">')<br />
<span class="keyword">end</span><br />
<br />
if prom1 == <span class="string">'pTet'</span><br />
try aTc = eval(retro)<br />
catch error(<span class="string">'Wrong aTc Value<span class="string">')<br />
<span class="keyword">end</span><br />
<br />
<span class="keyword">function</span> ydot = deriv(t,y)<span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pTet : y(6) = TetR ; retro = aTc<br />
</span> ydot = [f1(y(6), aTc);<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
elseif prom1 == <span class="string">'pFlhDC'</span><br />
if retro == <span class="string">'OmpR'</span><br />
<span class="keyword">function</span> ydot = deriv(t,y) <span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pFlhDC : y(6) = OmpR<br />
</span> ydot = [f3(y(2), y(6));<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
elseif retro == <span class="string">'EnvZ'</span><br />
<span class="keyword">function</span> ydot = deriv(t,y) <span class="comment"> % dy/dt<br />
</span> <span class="comment"> % pFlhDC : y(6) = EnvZ<br />
</span> ydot = [f3bis(y(6), y(2));<br />
f4(y(1), y(2));<br />
f5(y(1), y(2)) - gamma36;<br />
F(y(1), y(2)) - gamma37;<br />
f8(y(1), y(2)) - gamma38;<br />
f8(y(1), y(2));] - gamma*ones(6,1)<br />
<span class="keyword">end</span><br />
else<br />
error(<span class="string">'gene <span class="keyword">for</span> negative feed-back<span class="string">')<br />
<span class="keyword">end</span><br />
else<br />
error(<span class="string">'Wrong promoter <span class="keyword">for</span> flhDC<span class="string">')<br />
<span class="keyword">end</span><br />
<span class="keyword">end</span><br />
<br />
[t,labo]=ode45(deriv,t,init);<br />
<br />
<span class="comment">% The 'full modularity' of this Approach allow other variations, <br />
</span><span class="comment">% like changing the place of the negative feed-back<br />
</span><span class="comment">% (changing f8 by f7, f6, f5)...</span><br />
</pre></html><br />
<br />
</div></div>
Hugo
http://2008.igem.org/File:Hugo-Raguet.jpg
File:Hugo-Raguet.jpg
2008-10-30T04:54:29Z
<p>Hugo: uploaded a new version of "Image:Hugo-Raguet.jpg"</p>
<hr />
<div></div>
Hugo
http://2008.igem.org/File:Hugo-Raguet.jpg
File:Hugo-Raguet.jpg
2008-10-30T04:53:25Z
<p>Hugo: uploaded a new version of "Image:Hugo-Raguet.jpg"</p>
<hr />
<div></div>
Hugo
http://2008.igem.org/File:Cyprien.jpg
File:Cyprien.jpg
2008-10-30T04:52:16Z
<p>Hugo: uploaded a new version of "Image:Cyprien.jpg"</p>
<hr />
<div></div>
Hugo
http://2008.igem.org/File:Cyprien.jpg
File:Cyprien.jpg
2008-10-30T04:29:14Z
<p>Hugo: uploaded a new version of "Image:Cyprien.jpg"</p>
<hr />
<div></div>
Hugo
http://2008.igem.org/Team:Paris/Modeling/Others_prog
Team:Paris/Modeling/Others prog
2008-10-30T03:59:04Z
<p>Hugo: New page: <html> <style type="text/css"> pre {font-size: 1.2em} span.keyword {color: #0000FF} span.comment {color: #228B22} span.string {color: #A020F0} span.untermstring {color: #B20000} span.sysc...</p>
<hr />
<div><html><br />
<style type="text/css"><br />
<br />
pre {font-size: 1.2em}<br />
span.keyword {color: #0000FF}<br />
span.comment {color: #228B22}<br />
span.string {color: #A020F0}<br />
span.untermstring {color: #B20000}<br />
span.syscmd {color: #B28C00}<br />
}<br />
<br />
</style><br />
</html><br />
<br />
<div style="text-align: left"><br />
== complexes ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> complexes = complexes(x,y,K,n)<br />
<span class="comment">% amount of complexes n*x + y = x_-_y in function of x, y<br />
</span> <br />
<span class="comment">% x, y = initial amounts of binding molecules<br />
</span><span class="comment">% K = dissociation constant<br />
</span><span class="comment">% n = stoechiometric coefficient of x<br />
</span> <br />
syms <span class="string">z;</span><span class="comment"> % to treat z as a symbolic variable<br />
</span>Eqn = ( ( x - n*z )^n )*( y - z ) - K*z;<span class="comment"> % to define the equation in whose<br />
</span> <span class="comment"> % the amount of complexes is a root <br />
</span> <br />
S = eval(solve( Eqn, <span class="string">'z'</span> ));<span class="comment"> % the vector of the roots<br />
</span> <br />
Index = find ((0 < S) & (n*S < x) & (S < y) & (imag(S) == 0));<span class="comment"> % determine <br />
</span> <span class="comment"> % which<br />
</span> <span class="comment"> % root is <br />
</span> <span class="comment"> % acceptable<br />
</span> <br />
complexes = S(Index(1));<span class="comment"> % the result<br />
</span> <br />
<span class="keyword">end</span><br />
</pre></html><br />
<br />
== hill ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> compl = hill(x,K,n)<br />
<span class="comment">% complexation nx + Y = x_-_Y when x is in large excess :<br />
</span><span class="comment">% gives the ratio (x_-_Y)/(Ytotal) in function of x<br />
</span> <br />
<span class="comment">% x = molecule that binds to Y<br />
</span><span class="comment">% K^n = dissociation constant<br />
</span><span class="comment">% n = stoechiometric coefficient of x ; also known as 'cooperativity'<br />
</span> <br />
compl = x^n/(K^n + x^n);<br />
<br />
<span class="keyword">end</span><br />
</pre></html><br />
<br />
== Global ==<br />
<br />
</div></div>
Hugo
http://2008.igem.org/Team:Paris/Modeling/f3bisprog
Team:Paris/Modeling/f3bisprog
2008-10-30T03:57:33Z
<p>Hugo: /* find_&#131;3 ( FliA ) */</p>
<hr />
<div><html><br />
<style type="text/css"><br />
<br />
pre {font-size: 1.2em}<br />
span.keyword {color: #0000FF}<br />
span.comment {color: #228B22}<br />
span.string {color: #A020F0}<br />
span.untermstring {color: #B20000}<br />
span.syscmd {color: #B28C00}<br />
}<br />
<br />
</style><br />
</html><br />
<br />
<div style="text-align: left"><br />
== &#131;3bis ==<br />
<br />
<html><pre class="codeinput"><br />
<span class="keyword">function</span> act_pFlhDC = f3bis(EnvZ, FliA)<br />
<span class="comment">% expression of pTet in function of EnvZ and FliA<br />
</span> <br />
<span class="keyword">global</span> beta17 K15 n15 beta22 K6 n6 OmpR_b EnvZ_b K14 n14;<br />
<span class="comment">% parameters<br />
</span> <br />
OmpR_P = complexes((OmpR_b + EnvZ),EnvZ,K14,n14);<br />
<span class="comment">% Quantity of "phosphorylated OmpR"<br />
</span> <br />
act_pFlhDC = ( 1 - hill( OmpR_P, K15, n15 ) ) * ...<br />
(beta17 * (1 - hill( FliA, K6, n6)) + beta22 * hill( FliA, K6, n6) );<br />
<br />
<span class="keyword">end</span><br />
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Hugo
http://2008.igem.org/Team:Paris/Modeling/f2prog
Team:Paris/Modeling/f2prog
2008-10-30T03:57:04Z
<p>Hugo: /* find_&#131;3 ( FliA ) */</p>
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== &#131;2 ==<br />
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<span class="keyword">function</span> act_pBad = f2(arab)<br />
<span class="comment">% activity of pBad in function of arabinose<br />
</span> <br />
<span class="keyword">global</span> betabad Kbad nbad Kara nara;<br />
<span class="comment">% parameters<br />
</span> <br />
act_pBad = betabad * ( hill( hill( arab, Kara, nara ), Kbad, nbad ) );<br />
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<span class="keyword">end</span><br />
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Hugo
http://2008.igem.org/Team:Paris/Modeling/f8prog
Team:Paris/Modeling/f8prog
2008-10-30T03:56:34Z
<p>Hugo: New page: <html> <style type="text/css"> pre {font-size: 1.2em} span.keyword {color: #0000FF} span.comment {color: #228B22} span.string {color: #A020F0} span.untermstring {color: #B20000} span.sysc...</p>
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== &#131;8 ==<br />
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<span class="keyword">function</span> act_pFlhB = f8(FlhDC, FliA)<br />
<span class="comment">% expression of pFlhB in function of FlhDC and FliA<br />
</span> <br />
<span class="keyword">global</span> beta30 K5 n5 beta31 K11 n11;<br />
<span class="comment">% parameters<br />
</span> <br />
act_pFlhB = beta30 * hill( FlhDC, K5, n5 ) + beta31 * hill( FliA, K11, n11 );<br />
<br />
<span class="keyword">end</span><br />
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Hugo
http://2008.igem.org/Team:Paris/Modeling/f7prog
Team:Paris/Modeling/f7prog
2008-10-30T03:55:55Z
<p>Hugo: New page: <html> <style type="text/css"> pre {font-size: 1.2em} span.keyword {color: #0000FF} span.comment {color: #228B22} span.string {color: #A020F0} span.untermstring {color: #B20000} span.sysc...</p>
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== &#131;7 ==<br />
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<span class="keyword">function</span> act_pFlgB = f7(FlhDC, FliA)<br />
<span class="comment">% expression of pFlgB in function of FlhDC and FliA<br />
</span> <br />
<span class="keyword">global</span> beta28 K4 n4 beta29 K10 n10;<br />
<span class="comment">% parameters<br />
</span> <br />
act_pFlgB = beta28 * hill( FlhDC, K4, n4 ) + beta29 * hill( FliA, K10, n10 );<br />
<br />
<span class="keyword">end</span><br />
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Hugo
http://2008.igem.org/Team:Paris/Modeling/f6prog
Team:Paris/Modeling/f6prog
2008-10-30T03:55:14Z
<p>Hugo: New page: <html> <style type="text/css"> pre {font-size: 1.2em} span.keyword {color: #0000FF} span.comment {color: #228B22} span.string {color: #A020F0} span.untermstring {color: #B20000} span.sysc...</p>
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== &#131;6 ==<br />
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<span class="keyword">function</span> act_pFlgA = f6(FlhDC, FliA)<br />
<span class="comment">% expression of pFlgA in function of FlhDC and FliA<br />
</span> <br />
<span class="keyword">global</span> beta26 K3 n3 beta27 K9 n9;<br />
<span class="comment">% parameters<br />
</span> <br />
act_pFlgA = beta26 * hill( FlhDC, K3, n3 ) + beta27 * hill( FliA, K9, n9 );<br />
<br />
<span class="keyword">end</span><br />
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Hugo
http://2008.igem.org/Team:Paris/Modeling/f5prog
Team:Paris/Modeling/f5prog
2008-10-30T03:54:27Z
<p>Hugo: New page: <html> <style type="text/css"> pre {font-size: 1.2em} span.keyword {color: #0000FF} span.comment {color: #228B22} span.string {color: #A020F0} span.untermstring {color: #B20000} span.sysc...</p>
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== &#131;5 ==<br />
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<span class="keyword">function</span> act_pFliL = f5(FlhDC, FliA)<br />
<span class="comment">% expression of pFliL in function of FlhDC and FliA<br />
</span> <br />
<span class="keyword">global</span> beta24 K2 n2 beta25 K8 n8;<br />
<span class="comment">% parameters<br />
</span> <br />
act_pFliL = beta24 * hill( FlhDC, K2, n2 ) + beta25 * hill( FliA, K8, n8 );<br />
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<span class="keyword">end</span><br />
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Hugo
http://2008.igem.org/Team:Paris/Modeling/f4prog
Team:Paris/Modeling/f4prog
2008-10-30T03:53:47Z
<p>Hugo: New page: <html> <style type="text/css"> pre {font-size: 1.2em} span.keyword {color: #0000FF} span.comment {color: #228B22} span.string {color: #A020F0} span.untermstring {color: #B20000} span.sysc...</p>
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== &#131;4 ==<br />
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<span class="keyword">function</span> act_pFliA = f4(FlhDC, FliA)<br />
<span class="comment">% expression of pFliA in function of FlhDC and FliA<br />
</span> <br />
<span class="keyword">global</span> beta18 K1 n1 beta23 K7 n7;<br />
<span class="comment">% parameters<br />
</span> <br />
act_pFliA = beta18 * hill( FlhDC, K1, n1 ) + beta23 * hill( FliA, K7, n7 );<br />
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<span class="keyword">end</span><br />
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Hugo
http://2008.igem.org/Team:Paris/Modeling/f3bisprog
Team:Paris/Modeling/f3bisprog
2008-10-30T03:53:00Z
<p>Hugo: New page: <html> <style type="text/css"> pre {font-size: 1.2em} span.keyword {color: #0000FF} span.comment {color: #228B22} span.string {color: #A020F0} span.untermstring {color: #B20000} span.sysc...</p>
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== find_&#131;3 ( ''FliA'' ) ==<br />
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<span class="keyword">function</span> act_pFlhDC = f3bis(EnvZ, FliA)<br />
<span class="comment">% expression of pTet in function of EnvZ and FliA<br />
</span> <br />
<span class="keyword">global</span> beta17 K15 n15 beta22 K6 n6 OmpR_b EnvZ_b K14 n14;<br />
<span class="comment">% parameters<br />
</span> <br />
OmpR_P = complexes((OmpR_b + EnvZ),EnvZ,K14,n14);<br />
<span class="comment">% Quantity of "phosphorylated OmpR"<br />
</span> <br />
act_pFlhDC = ( 1 - hill( OmpR_P, K15, n15 ) ) * ...<br />
(beta17 * (1 - hill( FliA, K6, n6)) + beta22 * hill( FliA, K6, n6) );<br />
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<span class="keyword">end</span><br />
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Hugo