MATLAB: Integration Tolerance Not Met in SimBiology after sbioaccelerate

SimBiologytolerance

I'm receiving this error when trying to simulate my model after using s sbioaccelerate using some dose objects, but not others:

Error using SBCompiler.SimulationObject/simulate Integration Tolerance Not Met.

Error in sbiosimulate (line 140) [t, x] = simobj.simulate(mobj, cs, variants, doses);

I can simulate the model fine before using simbioaccelerate. I am receiving these warnings as well, and I know which equations they are coming from. Although, The equations shouldnt be producing complex numbers.

The right-hand side of the system of SimBiology ODEs results in complex numbers. The imaginary part of the result will be ignored. The repeated assignment rules of the SimBiology model result in complex numbers. The imaginary part of the result will be ignored.

I'm not sure what sbioaccelerate could be doing that is causing this; any help on how to troubleshoot this would be appreciated.

Best Answer

In addition to Joe's excellent suggestion, here are my thoughts:

The complex numbers are the source of the problem. The accelerated version of the model likely results in NaNs in cases where the unaccelerated model results in complex numbers. These NaNs then lead to the integration errors.

Are you using sqrt or some sort or raising a number to a fractional exponent? If so, then you could get a complex number if the argument is ever negative. This can happen when a concentration is close to zero, but solver tolerances allow it to go slightly negative. One solution there is to replace x^n with max(0,x)^n.

If you are still unable to find the cause of the complex numbers, please feel free to share additional details or contact Technical Support. I may not see updates you post here, so also feel free to contact me via my user page if you don't get a response to a comment here.

Good luck!

-Arthur

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MATLAB: How to convert a .m script to .sbproj file

Hi Colton,

You can use the sbiosaveproject function to save the SimBiology model (and data) to a .sbproj file. For example,

model = sbmlimport ('oscillator.xml');    
simData = sbiosimulate(model);
sbiosaveproject oscillator.sbproj model simData;

Hope it helps, Joe

MATLAB: Condition in which one compartment does not affect the mass balance

Hi Kazutaka,

In the example you are following along with (https://www.mathworks.com/help/simbio/ug/model-views.html), the PK part of the model is determined by a one compartment model with linear clearance (the compartment Central, with species Drug_Central and elimination reaction reaction_1). The biophase of the drug is modeled in a separate compartment: Biophase, with species Drug_Biophase, and creation reaction reaction_3 and elimination reaction reaction_2. The assumption in this model is that the drug concentration in the biophase does not affect the drug concentration in the central compartment and thereby the mass balance. This concept is implemented through reaction_3 : the stoichiometry of the reaction (Drug_Central -> Drug_Central + Drug_Biophase) has Drug_Central on both sides of the arrow, ensuring that Drug_Central is not being 'consumed' by the reaction. In other words: the concentration of Drug_Central is not affected by reaction_3 and reaction_3 doesn't show up in the ODEs for Drug_Central. In the diagram, this is illustrated by the dashed line between Drug_Central and reaction_3.

The assumption that the Biophase compartment does or doesn't affect the mass balance is a modeling decision made by the authors of the paper referenced at the bottom of the example page. As such, there is no condition that I can say your model should comply with in order to say that the compartment doesn't affect mass balance. The example merely states how to implement this.

I hope that helps. Let me know if you have further questions.

Best,

Sietse

Best Answer

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