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Team:Paris/Collaborations
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Here you can find the Matlab code, with respect to the iGEM Open Source concept : | Here you can find the Matlab code, with respect to the iGEM Open Source concept : | ||
<br> | <br> | ||
| - | <I>'''function Delay_Device_Simple'''> | + | <I>'''function Delay_Device_Simple'''</I> |
| - | close all | + | close all |
| - | + | for k = 1:6 | |
| - | for k = 1:6 | + | H = k; |
| - | + | t0 = 0 ; | |
| - | H = k; | + | tf = 10 ; |
| - | + | x0 = [0 ; 0 ; 4000 ; 0]; | |
| - | t0 = 0 ; | + | [t, x] = ode23(@delaydevice, [t0:0.1:tf],x0,[],H); |
| - | + | subplot(3,2,k) | |
| - | tf = 10 ; | + | plot (t,x) |
| - | + | end | |
| - | x0 = [0 ; 0 ; 4000 ; 0]; | + | legend({'prot','lacI','TetR','TolRII'}); |
| - | + | function solver(k) | |
| - | [t, x] = ode23(@delaydevice, [t0:0.1:tf],x0,[],H); | + | end |
| - | + | function xd = delaydevice(t, x, H) | |
| - | subplot(3,2,k) | + | %Resolution of a differential system |
| - | + | % Dilution of proteins | |
| - | plot (t,x) | + | gamma = 1; |
| - | + | gammaLVA = 3; | |
| - | end | + | % pBad Activation |
| - | + | Ara = 10000; | |
| - | legend({'prot','lacI','TetR','TolRII'}); | + | beta1 = 4000; |
| - | + | beta2 = 4000; | |
| - | function solver(k) | + | K1 = 40; |
| - | + | K2 = 40; | |
| - | end | + | % pLac Repression |
| - | + | beta3 = 2000; | |
| - | + | K3 = 40; | |
| - | function xd = delaydevice(t, x, H) | + | % pTet Repression |
| - | + | beta4 = 2000; | |
| - | %Resolution of a differential system | + | K4 = 40; |
| - | + | xd = zeros(size(x)); | |
| - | + | xd(1) = -gamma*x(1)+ beta1*(Ara/K1)/(1+(Ara/K1)); %Protein creation | |
| - | % Dilution of proteins | + | xd(2) = -gammaLVA*x(2)+ beta2*(Ara/K2)/(1+(Ara/K2)); % lacI creation |
| - | + | xd(3) = -gamma*x(3)+ beta3*(K3/(K3+(x(2))^2)); % TetR creation | |
| - | gamma = 1; | + | xd(4) = -gamma*x(4)+ beta4*(K4/(K4+x(3))); % TolRII creation |
| - | + | end | |
| - | gammaLVA = 3; | + | end |
| - | + | ||
| - | + | ||
| - | + | ||
| - | % pBad Activation | + | |
| - | + | ||
| - | Ara = 10000; | + | |
| - | + | ||
| - | beta1 = 4000; | + | |
| - | + | ||
| - | beta2 = 4000; | + | |
| - | + | ||
| - | K1 = 40; | + | |
| - | + | ||
| - | K2 = 40; | + | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | % pLac Repression | + | |
| - | + | ||
| - | beta3 = 2000; | + | |
| - | + | ||
| - | K3 = 40; | + | |
| - | + | ||
| - | % pTet Repression | + | |
| - | + | ||
| - | beta4 = 2000; | + | |
| - | + | ||
| - | K4 = 40; | + | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | xd = zeros(size(x)); | + | |
| - | + | ||
| - | + | ||
| - | xd(1) = -gamma*x(1)+ beta1*(Ara/K1)/(1+(Ara/K1)); %Protein creation | + | |
| - | + | ||
| - | xd(2) = -gammaLVA*x(2)+ beta2*(Ara/K2)/(1+(Ara/K2)); % lacI creation | + | |
| - | + | ||
| - | xd(3) = -gamma*x(3)+ beta3*(K3/(K3+(x(2))^2)); % TetR creation | + | |
| - | + | ||
| - | xd(4) = -gamma*x(4)+ beta4*(K4/(K4+x(3))); % TolRII creation | + | |
| - | + | ||
| - | end | + | |
| - | + | ||
| - | + | ||
| - | end | + | |
Latest revision as of 03:45, 22 October 2009
iGEM > Paris > Home > Collaborations
Modeling collaborations
As it happened that we share with the BCCS-Bristol projet some similarities and especially on the modeling part we have decided to contact them in order to either find synergies or just to be sure not to make a redondant modeling work. Obviously it seems that we were not working on the same domain.
So in order to make a complete modelisation of the "project" we provided them unconditionally with the Mathlab source code of the production of vesicles.
Here you can find the Matlab code, with respect to the iGEM Open Source concept :
function Delay_Device_Simple
close all
for k = 1:6
H = k;
t0 = 0 ;
tf = 10 ;
x0 = [0 ; 0 ; 4000 ; 0];
[t, x] = ode23(@delaydevice, [t0:0.1:tf],x0,[],H);
subplot(3,2,k)
plot (t,x)
end
legend({'prot','lacI','TetR','TolRII'});
function solver(k)
end
function xd = delaydevice(t, x, H)
%Resolution of a differential system
% Dilution of proteins
gamma = 1;
gammaLVA = 3;
% pBad Activation
Ara = 10000;
beta1 = 4000;
beta2 = 4000;
K1 = 40;
K2 = 40;
% pLac Repression
beta3 = 2000;
K3 = 40;
% pTet Repression
beta4 = 2000;
K4 = 40;
xd = zeros(size(x));
xd(1) = -gamma*x(1)+ beta1*(Ara/K1)/(1+(Ara/K1)); %Protein creation
xd(2) = -gammaLVA*x(2)+ beta2*(Ara/K2)/(1+(Ara/K2)); % lacI creation
xd(3) = -gamma*x(3)+ beta3*(K3/(K3+(x(2))^2)); % TetR creation
xd(4) = -gamma*x(4)+ beta4*(K4/(K4+x(3))); % TolRII creation
end
end
Ethic collaborations
We wanted to support the debates around ethics in science, in fact we also developped several points with our specialist in epistemology.
Therefore answering the Valencia poll was the opportunity to widen our range of questions about biosciences, to share knowledge, and to prove that we feel concerned by the problem that ethics tackles.
All the team answered the poll and we are grateful to Valencia for rewarding us with a gold medal ^^
Software tool collaborations
In order to develop a fully operational tool we created a poll that we send to other igem team to ask if it could be a great help for them or not and if they have also advices and expectations concerning this software.
2 Teams answered :
We had some interactions with the Freiburg_software team, specially with Paul Staab. They have developed a synthetic biological software suite, based on Google's collaboration and communication tool Wave : SynBiowave. The actual version is 0.2 but it is a project with a great potential!
