SimBiology

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Hello All, I am having this error in my code. --> Error reported from ODE Compilation: Initial assignment rules and repeated assignment rules cannot create explicit or implicit algebraic loops (for example, 'x = y' and 'y = x'). Implicit references to compartments occur when referencing a species in concentration. The following rules introduce algebraic loops into the model: The equation is to calculate the mitocondria voltage based on the chemical pumps and electrodefusion. however, the reaction rates for these pumps depend on the miltocondria voltage. As a result, my code has algebraic loop problem. How should I work around this issue?

I run many simulations in a loop (global sensitivity analysis) and would like to terminate stuck simulations by setting 'MaximumWallClock' (there parameter sets which make a model stiff and difficult to solve). Is there a build in way to flag simulations terminated in such way? The reason for this is that I need to discard those results because it would falsify the analysis outcome.

To perform a sensitivity analysis I am running *.sbproj coded models using 'biosimulate' in a for-loop and see for some parameter combinations the following warning: Warning: The right-hand side of the system of SimBiology ODEs results in complex numbers. The imaginary part of the result will be ignored. > In sbioodeflux_298d036b_ba03_4469_9210_25b32c7bbb2b (line 44) In sbiosimulate (line 140) In GSA (line 107) Can I trust the solutions? If not, how can I exclude the solutiuons which resulted in the warning above, i.e. is there a way to find programatically if a warning was produced? Update I added assignment of NaN's in case of fatal errors but still don't know how to handle the warnings. try ... [t,y] = sbiosimulate(m1); f1(i,j) = trapz(t,y(:,varNo)); % f1 AUC f2(i,j) = y(end,varNo); % f2 endPoint catch me disp( getReport( me, 'extended', 'hyperlinks', 'on' ) ) f1(i,j) = NaN; f2(i,j) = NaN; disp('Found an error-----------------------') end

As per my question, I would like to be able to set up an output function to use with sbiosimulate. I couldn't find anything from my bit of online searching nor from the sbiosimulate documentation. If anyone who is more familiar with SimBiology could send an example I would appreciate it. For some reference, I am trying to set up a code to sample a parameter space and evaluate if a given position is viable (as in doesn't fail to evaluate or take too long to solve). The latter point is where I am having my issue as I don't know how to set up a timeout function without using the method from this post: How can I set a timeout for slow executing codes?. Also, the model I am using is rather large (~40 species, 150 parameters) so I would prefer to not have to convert it for use with the ODE solver suite. Thanks for any help or pointers you can give!

I know that I can set the MaxStep in the simulation settings for a sbiomodel: as in: set(cs1.SolverOptions, 'MaxStep', 0.1); % Initialize configset for analysis run. cs = getconfigset(m1, 'default'); % RUNSIMULATION simulate SimBiology model, m1. % Run simulation. data = sbiosimulate(m1, cs, [], []); How can I set the step size to a constant number instead of just a maximum?