Difference between revisions of "Team:Dundee/Modeling/Appendix1"

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<a href="https://2015.igem.org/Team:Dundee/Modeling/Appendix3"  class="btn btn-primary btn-lg pull-right" role="button">Appendix 3: Chromate Detector</a> 
 +
<a href="https://2015.igem.org/Team:Dundee/Modeling/Appendix2"  class="btn btn-primary btn-lg pull-right" role="button">Appendix 2: Fingerprint Aging </a> 
 +
 +
 +
 +
<div class="content"><pre class="codeinput">
 +
  <span class="comment"><h2>MATLAB code from haptosen.m file</h2>%Function to define the non-dimensionalised system of ODEs describing the</span>
 +
<span class="comment">%binding between Haptoglobin and Haemoglobin. u is a 4 dimensional vector</span>
 +
<span class="comment">%where;</span>
 +
<span class="comment">% u(1)=Hp (Haptoglobin concentration)</span>
 +
<span class="comment">% u(2)=alphaHemo (Free Hemoglobin)</span>
 +
<span class="comment">% u(3)=alphaHemo/Hapto complex (Haptoglobin + alphaHemo complex)</span>
 +
<span class="comment">% u(4)=Hemo/Hapto complex (Full hemo/hapto complex).</span>
 +
<span class="comment">% t is the time that the simulation is run over.</span>
 +
<span class="comment">% lambda represents the parameter in the system determined by binding rates nd initial concentration of haemoglobin.</span>
 +
<span class="comment">% gamma represents the parameter in the system determined by binding rates.</span>
 +
<span class="keyword">function</span> f = haptosen(t,u,lambda,gamma);
 +
<span class="comment">% define the system of ODEs by setting the vector f = left hand side of the system.</span>
 +
f = [u(3)-lambda.*u(1)*u(2);
 +
    u(3)-lambda.*u(1)*u(2);
 +
    -u(3)+lambda.*u(1)*u(2)-gamma.*u(3);
 +
    gamma.*u(3)];
 +
<span class="comment">% The function is then ended.</span>
 +
 +
<span class="keyword">end</span>
 +
<span class="comment">% This function can then be called in the run_haptosen.m file by using</span>
 +
<span class="comment">% @haptosen command.</span>
 +
 +
 +
 +
 +
 +
  <span class="comment"> <h2>MATLAB code from run_haptosen.m file</h2>File to perform sensitivity analysis for Haptoglobin and Haemoglobin</span>
 +
<span class="comment">% binding model.</span>
 +
<span class="comment">% a is the number of values chosen for each of the ranges of parameters.</span>
 +
<span class="comment">% Therefore 100 different values were chosen.</span>
 +
a=100;
 +
<span class="comment">%Lambda1 is the range of values for the parameter Lambda, chosen with the</span>
 +
<span class="comment">%expected value of (100/317)*0.3878494524 as the mean value.</span>
 +
lambda1=linspace(0,((100/317)*0.3878494524)*2,a);
 +
<span class="comment">%Gamma1 is the range of values for the parameter Gamma, chosen with the</span>
 +
<span class="comment">%expected value of (83/317) as the mean value.</span>
 +
gamma1=linspace(0,(83/317)*2,a);
 +
<span class="comment">%T is the final time of the simulation.</span>
 +
T=30;
 +
<span class="comment">% Store sets an empty matrix for the final concentrations of the complex</span>
 +
<span class="comment">% with the varied parameter values.</span>
 +
Store = zeros(a,a);
 +
<span class="comment">%figure(1) calls up a new figure.</span>
 +
figure(1)
 +
<span class="comment">% The for loop solves the ode system defined in haptosen function using ode23 for the range of values for both</span>
 +
<span class="comment">% parameters.</span>
 +
<span class="keyword">for</span> i=1:a
 +
    <span class="keyword">for</span> j=1:a
 +
        [t,u]=ode23(@haptosen,[0 T],[4.17 1 0 0],[],lambda1(a+1-i),gamma1(j));
 +
        Store(i,j) = u(end,4);
 +
<span class="comment">%        Store(i,j) = (u(3,4)-u(2,4))/(t(3)-t(2));</span>
 +
    <span class="keyword">end</span>
 +
<span class="keyword">end</span>
 +
<span class="comment">%imagesc plots the surf plot of the parameters and the complex</span>
 +
<span class="comment">%concentration.</span>
 +
imagesc(Store)
 +
<span class="comment">% xlabel and ylabel add labels to the plot.</span>
 +
xlabel(<span class="string">'Increasing \lambda'</span>,<span class="string">'FontSize'</span>,15,<span class="string">'FontWeight'</span>,<span class="string">'bold'</span>);
 +
ylabel(<span class="string">'Increasing \gamma'</span>,<span class="string">'FontSize'</span>,15,<span class="string">'FontWeight'</span>,<span class="string">'bold'</span>);
 +
<span class="comment">%set removes the x and y axis</span>
 +
set(gca,<span class="string">'YTick'</span>,[],<span class="string">'XTick'</span>,[]);
 +
<span class="comment">% The following lines add a colour bar with defined labal and text.</span>
 +
c=colorbar(<span class="string">'Ticks'</span>,[0,0.99],<span class="string">'TickLabels'</span>,{<span class="string">'None'</span>,<span class="string">'High'</span>},<span class="string">'FontSize'</span>,15,<span class="string">'FontWeight'</span>,<span class="string">'bold'</span>);
 +
c.Label.String = <span class="string">'Complex Concentration'</span>;
 +
<span class="comment">%the following lines add a text arrow to allow for annotation of the graph with defined colours positions and width.</span>
 +
ta1 = annotation(<span class="string">'textarrow'</span>, [0.13 0.79], [0.13 0.92]);
 +
h = text(0.5,0.5,<span class="string">'Complex Formation'</span>);
 +
s = h.FontSize;
 +
h.FontSize = 12;
 +
j = h.Rotation;
 +
h.Rotation=45;
 +
k = h.Position;
 +
h.Position = [0.5 0.5 0];
 +
b = ta1.Color;
 +
d=ta1.LineWidth;
 +
ta1.Color = <span class="string">'red'</span>;
 +
ta1.LineWidth= 4;
 +
</pre><!--##### SOURCE BEGIN #####
 +
%Function to define the non-dimensionalised system of ODEs describing the
 +
%binding between Haptoglobin and Haemoglobin. u is a 4 dimensional vector
 +
%where; 
 +
% u(1)=Hp (Haptoglobin concentration)
 +
% u(2)=alphaHemo (Free Hemoglobin)
 +
% u(3)=alphaHemo/Hapto complex (Haptoglobin + alphaHemo complex)
 +
% u(4)=Hemo/Hapto complex (Full hemo/hapto complex).
 +
% t is the time that the simulation is run over.
 +
% lambda represents the parameter in the system determined by binding rates nd initial concentration of haemoglobin.
 +
% gamma represents the parameter in the system determined by binding rates.
 +
function f = haptosen(t,u,lambda,gamma);
 +
% define the system of ODEs by setting the vector f = left hand side of the system.
 +
f = [u(3)-lambda.*u(1)*u(2);
 +
    u(3)-lambda.*u(1)*u(2);
 +
    -u(3)+lambda.*u(1)*u(2)-gamma.*u(3);
 +
    gamma.*u(3)];
 +
% The function is then ended.
 +
 +
end
 +
% This function can then be called in the run_haptosen.m file by using
 +
% @haptosen command.
 +
##### SOURCE END #####
 +
##### SOURCE BEGIN #####
 +
% File to perform sensitivity analysis for Haptoglobin and Haemoglobin
 +
% binding model.
 +
% a is the number of values chosen for each of the ranges of parameters.
 +
% Therefore 100 different values were chosen.
 +
a=100;
 +
%Lambda1 is the range of values for the parameter Lambda, chosen with the
 +
%expected value of (100/317)*0.3878494524 as the mean value.
 +
lambda1=linspace(0,((100/317)*0.3878494524)*2,a);
 +
%Gamma1 is the range of values for the parameter Gamma, chosen with the
 +
%expected value of (83/317) as the mean value.
 +
gamma1=linspace(0,(83/317)*2,a);
 +
%T is the final time of the simulation.
 +
T=30;
 +
% Store sets an empty matrix for the final concentrations of the complex
 +
% with the varied parameter values.
 +
Store = zeros(a,a);
 +
%figure(1) calls up a new figure.
 +
figure(1)
 +
% The for loop solves the ode system defined in haptosen function using ode23 for the range of values for both
 +
% parameters.
 +
for i=1:a
 +
    for j=1:a
 +
        [t,u]=ode23(@haptosen,[0 T],[4.17 1 0 0],[],lambda1(a+1-i),gamma1(j));
 +
        Store(i,j) = u(end,4);
 +
%        Store(i,j) = (u(3,4)-u(2,4))/(t(3)-t(2));
 +
    end
 +
end
 +
%imagesc plots the surf plot of the parameters and the complex
 +
%concentration.
 +
imagesc(Store)
 +
% xlabel and ylabel add labels to the plot.
 +
xlabel('Increasing \lambda','FontSize',15,'FontWeight','bold');
 +
ylabel('Increasing \gamma','FontSize',15,'FontWeight','bold');
 +
%set removes the x and y axis
 +
set(gca,'YTick',[],'XTick',[]);
 +
% The following lines add a colour bar with defined labal and text.
 +
c=colorbar('Ticks',[0,0.99],'TickLabels',{'None','High'},'FontSize',15,'FontWeight','bold');
 +
c.Label.String = 'Complex Concentration';
 +
%the following lines add a text arrow to allow for annotation of the graph with defined colours positions and width.
 +
ta1 = annotation('textarrow', [0.13 0.79], [0.13 0.92]);
 +
h = text(0.5,0.5,'Complex Formation');
 +
s = h.FontSize;
 +
h.FontSize = 12;
 +
j = h.Rotation;
 +
h.Rotation=45;
 +
k = h.Position;
 +
h.Position = [0.5 0.5 0];
 +
b = ta1.Color;
 +
d=ta1.LineWidth;
 +
ta1.Color = 'red';
 +
ta1.LineWidth= 4;
 +
 +
 +
##### SOURCE END #####
 +
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Revision as of 13:45, 9 August 2015

run_haptosen

Lorem Ipsum

Appendix 3: Chromate Detector Appendix 2: Fingerprint Aging 
  
MATLAB code from haptosen.m file
%Function to define the non-dimensionalised system of ODEs describing the
%binding between Haptoglobin and Haemoglobin. u is a 4 dimensional vector
%where;
% u(1)=Hp (Haptoglobin concentration)
% u(2)=alphaHemo (Free Hemoglobin)
% u(3)=alphaHemo/Hapto complex (Haptoglobin + alphaHemo complex)
% u(4)=Hemo/Hapto complex (Full hemo/hapto complex).
% t is the time that the simulation is run over.
% lambda represents the parameter in the system determined by binding rates nd initial concentration of haemoglobin.
% gamma represents the parameter in the system determined by binding rates.
function f = haptosen(t,u,lambda,gamma);
% define the system of ODEs by setting the vector f = left hand side of the system.
f = [u(3)-lambda.*u(1)*u(2);
    u(3)-lambda.*u(1)*u(2);
    -u(3)+lambda.*u(1)*u(2)-gamma.*u(3);
    gamma.*u(3)];
% The function is then ended.

end
% This function can then be called in the run_haptosen.m file by using
% @haptosen command.





   
MATLAB code from run_haptosen.m file
File to perform sensitivity analysis for Haptoglobin and Haemoglobin
% binding model.
% a is the number of values chosen for each of the ranges of parameters.
% Therefore 100 different values were chosen.
a=100;
%Lambda1 is the range of values for the parameter Lambda, chosen with the
%expected value of (100/317)*0.3878494524 as the mean value.
lambda1=linspace(0,((100/317)*0.3878494524)*2,a);
%Gamma1 is the range of values for the parameter Gamma, chosen with the
%expected value of (83/317) as the mean value.
gamma1=linspace(0,(83/317)*2,a);
%T is the final time of the simulation.
T=30;
% Store sets an empty matrix for the final concentrations of the complex
% with the varied parameter values.
Store = zeros(a,a);
%figure(1) calls up a new figure.
figure(1)
% The for loop solves the ode system defined in haptosen function using ode23 for the range of values for both
% parameters.
for i=1:a
    for j=1:a
        [t,u]=ode23(@haptosen,[0 T],[4.17 1 0 0],[],lambda1(a+1-i),gamma1(j));
        Store(i,j) = u(end,4);
%         Store(i,j) = (u(3,4)-u(2,4))/(t(3)-t(2));
    end
end
%imagesc plots the surf plot of the parameters and the complex
%concentration.
imagesc(Store)
% xlabel and ylabel add labels to the plot.
xlabel('Increasing \lambda','FontSize',15,'FontWeight','bold');
ylabel('Increasing \gamma','FontSize',15,'FontWeight','bold');
%set removes the x and y axis
set(gca,'YTick',[],'XTick',[]);
% The following lines add a colour bar with defined labal and text.
c=colorbar('Ticks',[0,0.99],'TickLabels',{'None','High'},'FontSize',15,'FontWeight','bold');
c.Label.String = 'Complex Concentration';
%the following lines add a text arrow to allow for annotation of the graph with defined colours positions and width.
ta1 = annotation('textarrow', [0.13 0.79], [0.13 0.92]);
h = text(0.5,0.5,'Complex Formation');
s = h.FontSize;
h.FontSize = 12;
j = h.Rotation;
h.Rotation=45;
k = h.Position;
h.Position = [0.5 0.5 0];
b = ta1.Color;
d=ta1.LineWidth;
ta1.Color = 'red';
ta1.LineWidth= 4;

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<highlight class="highlight">Dry Lab</highlight>

<highlight class="highlight">Appendix 1: BioSpray Code</highlight>

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Lorem Ipsum


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<a href="https://2015.igem.org/Team:Dundee/Modeling/Appendix3" class="btn btn-primary btn-lg pull-right" role="button">Appendix 3: Chromate Detector</a> <a href="https://2015.igem.org/Team:Dundee/Modeling/Appendix2" class="btn btn-primary btn-lg pull-right" role="button">Appendix 2: Fingerprint Aging </a> 




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