Create script just for SSA

Author: dmitrisvetlov

WorkSpace/Dmitri/NFDP_SSA.m

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+%% Initial Setup
+
+close all
+clear all
+addpath(genpath('../../src'));
+
+M = [1 2 3 6]; % Number of intermediate states
+
+kOn = 0.1;
+kOff = kOn * 1000 / 2;
+
+tau = 50;
+delayPeriods = 10;
+tSpan = linspace(0, tau * delayPeriods, 1 + delayPeriods);
+
+Model = SSIT;
+Model.species = {'Dempty'; 'Dfull'; 'X'};
+
+initialConditionX = randi([15, 50]);
+Model.initialCondition = [1; 0; initialConditionX];
+
+parameters = ({...
+    'kPlus', 100; ... % (Delayed) rate of protein production
+    'kMinus', 1; ... % Rate of protein degradation
+    'kOn', kOn; ... % Rate of operator site emptying / activation
+    'kOff', kOff; ... % Rate of operator site filling / deactivation
+    'tau', tau ... % Delay in protein production
+    });
+Model.parameters = parameters;
+
+Model.propensityFunctions = {
+    'kOn*Dfull', ... % Operator site emptying
+    'kOff*Dempty*X', ... % Operator site filling
+    'kPlus*Dempty', ... % (Delayed) protein production
+    'kMinus*X' ... % Protein degradation
+    };
+
+Model.stoichiometry = [...
+     1, -1,  0,  0; ... % Dempty
+    -1,  1,  0,  0; ... % Dfull
+     0,  0,  1, -1 ... % X
+    ];
+
+% The only delayed reaction in the system is the third, with a delay equal
+% to tau. It has a single reactant, one Dempty, so we must include it in
+% the delayed-reaction scheduling stochiometries:
+
+Model.delayedReactions = [3, Model.parameters{5,2}];
+
+Model.delayedReactionSchedulingS = [...
+     0,  0, -1,  0; ... % Dempty
+     0,  0,  0,  0; ... % Dfull
+     0,  0,  0,  0 ... % X
+    ];
+
+%% Configure and run SSA
+
+Model.tSpan = tSpan;
+Model = Model.formPropensitiesGeneral('NFDP');
+
+Model.solutionScheme = 'SSA';
+
+% Number of independent data sets to generate.
+Model.ssaOptions.Nexp = 2;   
+
+% Number of cells to include at each time point for each data set.
+Model.ssaOptions.nSimsPerExpt = 3e4; 
+
+tic;
+SSAsoln = Model.solve([], 'ssa_out.csv');
+SSAtime = toc;
+
+save SSAtime.mat SSAtime
+save SSAsoln.mat SSAsoln