Team:Paris/Modeling/BOB/Simulations/Codes

From 2008.igem.org

(Difference between revisions)
m
 
(4 intermediate revisions not shown)
Line 1: Line 1:
{{Paris/Menu}}
{{Paris/Menu}}
-
* Here are the different MatLab codes used for our simulations
+
* Here are the different codes used for our simulations
-
= Oscillations Short System =
+
 
 +
 
= FIFO =
= FIFO =
* Code to Test the FIFO without FliA
* Code to Test the FIFO without FliA
Line 12: Line 13:
[[Image:FIFO_avec_FliA_code.jpg]]
[[Image:FIFO_avec_FliA_code.jpg]]
-
= Model Justification =
+
=Alternatives of the core system in BIOCHAM=
 +
<code><pre>
 +
%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)
 +
 
 +
</pre></code>

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)