Simbiology general stability and speed

2015 9 23
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I am interested in using simbiology to simulate ~96 to ~144 different chemical reactions related to the TCA cycle. They would all be solved simultaneously. I just tried out the simbiology toolbox. It seems very powerful, but I just did some very basic rxn kinetics. Does anyone have experience with simbiology? Could I expect it to handle this many equations simultaneously? I make the approximation that most reactions are first order, though some of them will be "ping-pong". Would such a simulation run faster if I just wrote it myself in matlab? Does simbiology put extra overhead on the processes? I would probably want to run the simulation for 100 to 500 different time points.

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Ingrid Tigges
Ingrid Tigges 2015-9-24
编辑：Ingrid Tigges 2015-9-24

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I have simulated models with more than 150 reactions myself in SimBiology and this works without problem. Have you seen the "accelerated" option in SimBiology (see http://www.mathworks.com/help/simbio/ref/sbioaccelerate.html)? I doubt your own MATLAB Code will be faster than using SimBiology with this option. If you run repeated simulations with this option it is not unlikely that your SimBiology model runs 10-20 times faster than self-written MATLAB code. Note that the acceleration itself takes some time meaning the first run can be slower than without acceleration.

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