SimBiology

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I have an .sbml model I want to simulate using ssa. It works for small timespans, and when using ode simulations. However, in this example matlab simply crashes. Why is this? is there a way of preventing this? % Load model. model_egfr_net = sbmlimport('egfr_net.xml'); % Prepare model for SSA simulations. clean_ssa_sbml_model(model_egfr_net) cs = getconfigset(model_egfr_net); cs.SolverType = 'ssa'; cs.StopTime = 100.0; % Simulate model. [t, x, names] = sbiosimulate(model_egfr_net); I have attached the model. Also, per https://uk.mathworks.com/matlabcentral/answers/1582584-simbio-running-stochastic-ssa-simulation-of-sbml-imported-model the model has to be modified to enable ssa simulations. The attached function (used in the script) is provided here: function [] = clean_ssa_sbml_model(model) parameters = sbioselect(model, 'Type', 'parameter'); for paramIndex = 1:numel(parameters) parameter = parameters(paramIndex); [~, usageTable] = findUsages(parameter); % Update any reaction that uses this parameter in its rate. if isempty(usageTable) % if check added by Torkel. continue end reactions = usageTable.Component(usageTable.Property == "ReactionRate"); for reactionIndex = 1:numel(reactions) reaction = reactions(reactionIndex); oldRate = reaction.ReactionRate; kineticLaw = reaction.KineticLaw; if isempty(kineticLaw) % Add a kinetic law kineticLaw = addkineticlaw(reaction, 'MassAction'); else % Update the existing kinetic law to mass action kineticLaw.KineticLawName = 'MassAction'; end kineticLaw.ParameterVariableNames = parameter.Name; newRate = reaction.ReactionRate; if ~strcmp(oldRate, newRate) warning("Reaction rate for reaction %s changed from %s to %s.", ... reaction.Name, oldRate, newRate); end end end end

HI there, Q1: i'm wondering if there are two distinct ODE models and each representing a biological system that may have some relationship together (for example cell cycle pathway and apoptosis pathway), is it possible to mix them in one model using the parameters and initial values same as the original model (without changing the parameters)? Because there are some mutual elements in these models, the modelers made some assumption to get a correct dynamics. So, when you combine the two model, the dynamic of a particular element (X) will be different (incorrect). Q2: My question is that since the dynamics of element X in each of these single models is correct, is it possible to give the correct time course (dynamic) of X to SIMBIOLOGY in order to have the correct dynamic at last(and Simbiology probably fine-tunes some other parameters)? Q3: Is it possible that this process makes the dynamics of other species in the model incorrect? Q4: And another question is that if it is possible to fix some parameters (known parameters) and want Simbiology to just estimate the unknown parameters (and we may have the dynamics of some of the species but not all)? Q5: I remember that I tried to give one time course (of one specie) to simbilogy but the answer was quite wrong! DO you know why it may happens?