Team:Paris/Modeling/BOB/Simulations/Codes

From 2008.igem.org

(Difference between revisions)
(→Alternatives of the core system in BIOCHAM)
Line 18: Line 18:
MA(gamma) for Flia => _.
MA(gamma) for Flia => _.
MA(gamma) for FlhDC => _.
MA(gamma) for FlhDC => _.
-
MA(gamma) for TetR => _.
+
MA(gamma) for EnvZ => _.
%FlhDC action
%FlhDC action
MA(beta_Flia) for FlhDC => Flia + FlhDC.
MA(beta_Flia) for FlhDC => Flia + FlhDC.
-
MA(beta_TetR) for FlhDC => TetR + FlhDC.
+
MA(beta_EnvZ) for FlhDC => TetR + FlhDC.
%Flia action
%Flia action
MA(betap_Flia) for Flia => Flia + Flia.
MA(betap_Flia) for Flia => Flia + Flia.
-
MA(betap_TetR) for Flia => TetR + Flia.
+
MA(betap_EnvZ) for Flia => EnvZ + Flia.
%TetR action
%TetR action
-
beta_FlhDC*(theta_FlhDC^n)/(theta_FlhDC^n+[TetR]^n) for _  => FlhDC.
+
beta_FlhDC*(theta_FlhDC^n)/(theta_FlhDC^n+[EnvZ]^n) for _  => FlhDC.
parameter(gamma,1).
parameter(gamma,1).
parameter(beta_Flia,0.1429).
parameter(beta_Flia,0.1429).
parameter(betap_Flia,0.8581).
parameter(betap_Flia,0.8581).
-
parameter(beta_TetR,0.2222).
+
parameter(beta_EnvZ,0.2222).
-
parameter(betap_TetR,0.7778).
+
parameter(betap_EnvZ,0.7778).
parameter(beta_FlhDC,1).
parameter(beta_FlhDC,1).
-
parameter(theta_FlhDC,0.1).
+
parameter(theta_FlhDC,0.5).
parameter(n,4).
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)
</pre></code>
</pre></code>

Revision as of 22:55, 29 October 2008

  • Here are the different MatLab 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)
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