Edinburgh/DivisionPopper/Modelling/Edinburgh/PRISMCode
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- | 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 [[ | + | This is the [http://www.prismmodelchecker.org/ 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 [[Edinburgh/DivisionPopper/Modelling|Modelling]] section. |
== The PRISM Code == | == The PRISM Code == | ||
- | ctmc | + | ''ctmc'' |
+ | |||
+ | // maximal number of YFP molecules in the model | ||
const int maxYFP=500; | const int maxYFP=500; | ||
+ | |||
+ | // maximal number of GFP molecules in the model | ||
+ | |||
const int maxGFP=500; | const int maxGFP=500; | ||
+ | // reate for the forward phase duration | ||
const double forwardPhaseRate =0.0001; | const double forwardPhaseRate =0.0001; | ||
+ | |||
+ | // rate for the backward phase duration | ||
const double backwardPhaseRate =0.0001; | const double backwardPhaseRate =0.0001; | ||
+ | |||
+ | // rate for the flipping phase duartion | ||
const double flipPhaseRate =0.0001; | const double flipPhaseRate =0.0001; | ||
+ | |||
+ | // rate of YPF expression | ||
const double expYFP =0.1; | const double expYFP =0.1; | ||
+ | |||
+ | //rate of the GFP expression | ||
+ | |||
const double expGFP =0.1; | const double expGFP =0.1; | ||
+ | |||
+ | // rate of the YFP degradation | ||
const double degYFP =0.001; | const double degYFP =0.001; | ||
+ | |||
+ | // rate of he GFP degradation | ||
+ | |||
const double degGFP =0.001; | const double degGFP =0.001; | ||
- | module YFP | + | //module representing YFP molecules and actions |
+ | |||
+ | ''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; | ||
- | endmodule | + | ''endmodule'' |
- | module GFP | + | //module representing GFP molecules and actions |
+ | |||
+ | ''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; | ||
- | endmodule | + | ''endmodule'' |
- | module Phase | + | |
+ | //module representing the Phases' state | ||
+ | |||
+ | ''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; | [changeFromFlipToBackward] (phase=1) -> flipPhaseRate : phase'= 2; | ||
- | endmodule | + | ''endmodule'' |
Latest revision as of 17:04, 4 October 2007
This is the [http://www.prismmodelchecker.org/ 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
// maximal number of YFP molecules in the model
const int maxYFP=500;
// maximal number of GFP molecules in the model
const int maxGFP=500;
// reate for the forward phase duration const double forwardPhaseRate =0.0001;
// rate for the backward phase duration const double backwardPhaseRate =0.0001;
// rate for the flipping phase duartion const double flipPhaseRate =0.0001;
// rate of YPF expression
const double expYFP =0.1;
//rate of the GFP expression
const double expGFP =0.1;
// rate of the YFP degradation
const double degYFP =0.001;
// rate of he GFP degradation
const double degGFP =0.001;
//module representing YFP molecules and actions
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 representing GFP molecules and actions
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 representing the Phases' state
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