Team:Paris/Modeling/More f1 Algo

From 2008.igem.org

(Difference between revisions)
(→Inv_ƒ1)
(→find_ƒ1)
 
Line 17: Line 17:
<html><pre class="codeinput">
<html><pre class="codeinput">
-
<span class="keyword">function</span> act_pTet = f1(TetR, aTc)
+
<span class="keyword">function</span> optimal_parameters = find_f1(X_data, Y_data, initial_parameters)
-
<span class="comment">% activity of pTet in function of TetR and aTc
+
<span class="comment">% gives the 'best parameters' involved in f1 by least-square optimisation
</span>  
</span>  
-
<span class="keyword">global</span> beta16 K13 n13 K12 n12;
+
<span class="comment">% X_data = vector of given values of a [aTc]i (experimentally
-
<span class="comment">% parameters
+
</span><span class="comment">% controled)
 +
</span><span class="comment">% Y_data = vector of experimentally measured values f1 corresponding of
 +
</span><span class="comment">% the X_data
 +
</span><span class="comment">% initial_parameters = values of the parameters proposed by the literature
 +
</span><span class="comment">%                      or simply guessed
 +
</span><span class="comment">%                    = [beta16, (K13 -> (gamma.K13)/(coefTet.f0)), n13, K12, n12]
</span>  
</span>  
-
act_pTet = beta16 * ( 1 - hill( TetR*(1 - hill( aTc, K13, n13 )), K12, n12 ) );
+
<span class="comment">% Warning : in the global parameters, K20 -> K20/coefTet
 +
</span>
 +
    <span class="keyword">function</span> output = expr_pTet(parameters, X_data)
 +
        <span class="keyword">for</span> k = 1:length(X_data)
 +
                output(k) = parameters(1) * (1 - ...
 +
                    hill((1 - hill(X_data(k),parameters(4),parameters(5))),parameters(2),parameters(3)));
 +
        <span class="keyword">end</span>
 +
    <span class="keyword">end</span>
   
   
 +
options=optimset(<span class="string">'LevenbergMarquardt'</span>,<span class="string">'on'</span>,<span class="string">'TolX'</span>,1e-10,<span class="string">'MaxFunEvals'</span>,1e10,<span class="string">'TolFun'</span>,1e-10,<span class="string">'MaxIter'</span>,1e4);
 +
<span class="comment">% options for the function lsqcurvefit
 +
</span>
 +
optimal_parameters = lsqcurvefit( @(parameters, X_data) expr_pTet(parameters, X_data), ...
 +
    initial_parameters, X_data, Y_data, 1/10*initial_parameters, 10*initial_parameters, options );
 +
<span class="comment">% search for the fittest parameters, between 1/10 and 10 times the initial
 +
</span><span class="comment">% parameters
 +
</span>
<span class="keyword">end</span>
<span class="keyword">end</span>
</pre></html>
</pre></html>

Latest revision as of 03:47, 30 October 2008

find_ƒ1 

function optimal_parameters = find_f1(X_data, Y_data, initial_parameters)
% gives the 'best parameters' involved in f1 by least-square optimisation
 
% X_data = vector of given values of a [aTc]i (experimentally
% controled)
% Y_data = vector of experimentally measured values f1 corresponding of
% the X_data
% initial_parameters = values of the parameters proposed by the literature
%                       or simply guessed
%                    = [beta16, (K13 -> (gamma.K13)/(coefTet.f0)), n13, K12, n12]
 
% Warning : in the global parameters, K20 -> K20/coefTet
 
     function output = expr_pTet(parameters, X_data)
         for k = 1:length(X_data)
                 output(k) = parameters(1) * (1 - ...
                     hill((1 - hill(X_data(k),parameters(4),parameters(5))),parameters(2),parameters(3)));
         end
     end
 
options=optimset('LevenbergMarquardt','on','TolX',1e-10,'MaxFunEvals',1e10,'TolFun',1e-10,'MaxIter',1e4);
% options for the function lsqcurvefit
 
optimal_parameters = lsqcurvefit( @(parameters, X_data) expr_pTet(parameters, X_data), ...
     initial_parameters, X_data, Y_data, 1/10*initial_parameters, 10*initial_parameters, options );
% search for the fittest parameters, between 1/10 and 10 times the initial
% parameters
 
end

Inv_ƒ1 

function quant_aTc = Inv_f1(inducer_quantity)
% gives the quantity of [aTc]i needed to get inducer_quantity of a protein
% throught a gene behind pTet
 
global gamma, f0;
% parameters
 
     function equa = F(x)
         equa = f1( (f0/gamma) , x ) - inducer_quantity;
     end
 
options=optimset('LevenbergMarquardt','on','TolX',1e-10,'MaxFunEvals',1e10,'TolFun',1e-10,'MaxIter',1e4);
 
quant_aTc = fsolve(F,1,options);
 
end

Retrieved from "http://2008.igem.org/Team:Paris/Modeling/More_f1_Algo"