Team:Paris/Modeling/BOB/Simulations/Codes

From 2008.igem.org

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(New page: {{Paris/Menu}} * Here are the different MatLab codes used for our simulations = FIFO = * Code to Test the FIFO without FliA '' beta=[1200/1450 150/450 100/450 50/350]; %% parameters valu...)
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{{Paris/Menu}}
{{Paris/Menu}}
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* Here are the different MatLab codes used for our simulations
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* Here are the different codes used for our simulations
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= FIFO =
= FIFO =
* Code to Test the FIFO without FliA
* Code to Test the FIFO without FliA
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''
 
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beta=[1200/1450 150/450 100/450 50/350]; %% parameters value
 
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Tspan=[0:0.1:40]
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[[Image:FIFO_sans_FliA_code.jpg]]
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* Code to Test the FIFO with FliA
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%% function to generate FlhDC evolution
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[[Image:FIFO_avec_FliA_code.jpg]]
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    function Y = step(T)
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=Alternatives of the core system in BIOCHAM=
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        for i = 1:length(T)
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<code><pre>
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            if (T(i) < 20)
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%degradations
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                Y(i) = 1;
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MA(gamma) for Flia => _.
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            else
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MA(gamma) for FlhDC => _.
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                Y(i) = 0;
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MA(gamma) for EnvZ => _.
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            end
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        end
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    end
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%% function to set the equations
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    function Y = Vp(t,V)
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        Y(4,1)=0;
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        for i = 1:3
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            Y(i,1) = beta(i) * V(5) + ((1-beta(i)) * V(4)) - V(i);
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        end
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        Y(5,1) = step(t) - V(5);
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    end
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C0=zeros(5,1); %% initial conditions
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%% ODE solver
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[bar C]=ode23(@Vp,Tspan,C0);
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plot(Tspan,C)
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legend('CFP','YFP','RFP','FliA','FlhDC')
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end
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''
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* Code to Test the FIFO without FliA
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''
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beta=[1200/1450 150/450 100/450 50/350]; %% parameters value
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Tspan=[0:0.1:40]
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%FlhDC action
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MA(beta_Flia) for FlhDC => Flia + FlhDC.
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MA(beta_EnvZ) for FlhDC => TetR + FlhDC.
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%Flia action
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MA(betap_Flia) for Flia => Flia + Flia.
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MA(betap_EnvZ) for Flia => EnvZ + Flia.
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%% function to generate FlhDC evolution
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%TetR action
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beta_FlhDC*(theta_FlhDC^n)/(theta_FlhDC^n+[EnvZ]^n) for _  => FlhDC.
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    function Y = step(T)
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parameter(gamma,1).
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        for i = 1:length(T)
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parameter(beta_Flia,0.1429).
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            if (T(i) < 20)
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parameter(betap_Flia,0.8581).
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                Y(i) = 1;
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parameter(beta_EnvZ,0.2222).
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            else
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parameter(betap_EnvZ,0.7778).
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                Y(i) = 0;
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parameter(beta_FlhDC,1).
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            end
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parameter(theta_FlhDC,0.5).
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        end
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parameter(n,4).
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    end
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%% function to set the equations
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%Alternative 1
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    function Y = Vp(t,V)
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%parameter(beta_Flia,1).
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        for i = 1:4
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%parameter(betap_Flia,0).
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            Y(i,1) = beta(i) * V(5) + ((1-beta(i)) * V(4)) - V(i);
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        end
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        Y(5,1) = step(t) - V(5);
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    end
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C0=zeros(5,1); %% initial conditions
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%Alternative 2
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%parameter(beta_EnvZ,0).
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%parameter(betap_EnvZ,1).
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%% ODE solver
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%Alternative 3
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[bar C]=ode23(@Vp,Tspan,C0);
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%parameter(theta_FlhDC,0.1)
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plot(Tspan,C)
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</pre></code>
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legend('CFP','YFP','RFP','FliA','FlhDC')
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end''
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Latest revision as of 23:04, 29 October 2008

  • Here are the different codes used for our simulations


FIFO

  • Code to Test the FIFO without FliA

FIFO sans FliA code.jpg

  • Code to Test the FIFO with FliA

FIFO avec FliA code.jpg

Alternatives of the core system in BIOCHAM

%degradations
MA(gamma) for Flia => _.
MA(gamma) for FlhDC => _.
MA(gamma) for EnvZ => _.

%FlhDC action
MA(beta_Flia) for FlhDC => Flia + FlhDC.
MA(beta_EnvZ) for FlhDC => TetR + FlhDC.

%Flia action
MA(betap_Flia) for Flia => Flia + Flia.
MA(betap_EnvZ) for Flia => EnvZ + Flia.

%TetR action
beta_FlhDC*(theta_FlhDC^n)/(theta_FlhDC^n+[EnvZ]^n) for _  => FlhDC.

parameter(gamma,1).
parameter(beta_Flia,0.1429).
parameter(betap_Flia,0.8581).
parameter(beta_EnvZ,0.2222).
parameter(betap_EnvZ,0.7778).
parameter(beta_FlhDC,1).
parameter(theta_FlhDC,0.5).
parameter(n,4).

%Alternative 1
%parameter(beta_Flia,1).
%parameter(betap_Flia,0).

%Alternative 2
%parameter(beta_EnvZ,0).
%parameter(betap_EnvZ,1).

%Alternative 3
%parameter(theta_FlhDC,0.1)
Retrieved from "http://2008.igem.org/Team:Paris/Modeling/BOB/Simulations/Codes"