Edinburgh/DivisionPopper/Modelling/Edinburgh/PRISMCode

From 2007.igem.org

(Difference between revisions)
(The PRISM Code)
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== The PRISM Code ==
== The PRISM Code ==
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ctmc
+
''ctmc''
const int maxYFP=500;
const int maxYFP=500;
 +
const int maxGFP=500;
const int maxGFP=500;
const double forwardPhaseRate =0.0001;
const double forwardPhaseRate =0.0001;
 +
const double backwardPhaseRate =0.0001;
const double backwardPhaseRate =0.0001;
 +
const double flipPhaseRate =0.0001;
const double flipPhaseRate =0.0001;
const double expYFP =0.1;
const double expYFP =0.1;
 +
const double expGFP =0.1;
const double expGFP =0.1;
const double degYFP =0.001;
const double degYFP =0.001;
 +
const double degGFP =0.001;
const double degGFP =0.001;
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module YFP
+
''module YFP''
levelYFP:[0..maxYFP] init 0;
levelYFP:[0..maxYFP] init 0;
 +
[degYFP] (levelYFP>0) -> degYFP * levelYFP : levelYFP' = levelYFP-1;
[degYFP] (levelYFP>0) -> degYFP * levelYFP : levelYFP' = levelYFP-1;
 +
[expYFP] (phase=0)&(levelYFP<maxYFP) -> expYFP : levelYFP' = levelYFP+1;
[expYFP] (phase=0)&(levelYFP<maxYFP) -> expYFP : levelYFP' = levelYFP+1;
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endmodule
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''endmodule''
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module GFP
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''module GFP''
levelGFP:[0..maxGFP] init 0;
levelGFP:[0..maxGFP] init 0;
 +
[degGFP] (levelGFP>0)-> degGFP * levelGFP : levelGFP'=levelGFP-1;
[degGFP] (levelGFP>0)-> degGFP * levelGFP : levelGFP'=levelGFP-1;
 +
[expGFP] (phase=2)&(levelGFP<maxGFP) -> expGFP : levelGFP'=levelGFP+1;
[expGFP] (phase=2)&(levelGFP<maxGFP) -> expGFP : levelGFP'=levelGFP+1;
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endmodule
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''endmodule''
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module Phase
+
 
 +
''module Phase''
phase:[0..3] init 0;
phase:[0..3] init 0;
 +
[changeFromForwardToFlip]  (phase=0) -> forwardPhaseRate : phase'=1;
[changeFromForwardToFlip]  (phase=0) -> forwardPhaseRate : phase'=1;
 +
[changeFromBackwardToFlip] (phase=2) -> backwardPhaseRate : phase'=3;
[changeFromBackwardToFlip] (phase=2) -> backwardPhaseRate : phase'=3;
 +
[changeFromFlipToForward]  (phase=3) -> flipPhaseRate : phase'= 0;
[changeFromFlipToForward]  (phase=3) -> flipPhaseRate : phase'= 0;
-
[changeFromFlipToBackward] (phase=1) -> flipPhaseRate : phase'= 2;
 
-
endmodule
+
[changeFromFlipToBackward] (phase=1) -> flipPhaseRate : phase'= 2;
 +
''
 +
endmodule''

Revision as of 13:04, 27 September 2007

This is the PRISM code we developed for simulation and model checking of the stochastic model. It is a implementation of the Underlying Markov Chain of the Process Algebra model reported in the Modelling section.

The PRISM Code

ctmc

const int maxYFP=500;

const int maxGFP=500;

const double forwardPhaseRate =0.0001;

const double backwardPhaseRate =0.0001;

const double flipPhaseRate =0.0001;

const double expYFP =0.1;

const double expGFP =0.1;

const double degYFP =0.001;

const double degGFP =0.001;


module YFP

levelYFP:[0..maxYFP] init 0;

[degYFP] (levelYFP>0) -> degYFP * levelYFP : levelYFP' = levelYFP-1;

[expYFP] (phase=0)&(levelYFP<maxYFP) -> expYFP : levelYFP' = levelYFP+1;

endmodule


module GFP

levelGFP:[0..maxGFP] init 0;

[degGFP] (levelGFP>0)-> degGFP * levelGFP : levelGFP'=levelGFP-1;

[expGFP] (phase=2)&(levelGFP<maxGFP) -> expGFP : levelGFP'=levelGFP+1;

endmodule


module Phase

phase:[0..3] init 0;

[changeFromForwardToFlip] (phase=0) -> forwardPhaseRate : phase'=1;

[changeFromBackwardToFlip] (phase=2) -> backwardPhaseRate : phase'=3;

[changeFromFlipToForward] (phase=3) -> flipPhaseRate : phase'= 0;

[changeFromFlipToBackward] (phase=1) -> flipPhaseRate : phase'= 2; endmodule