SimBiology :: controlling a species concentration using a custom user-defined input function

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Andrew Sundstrom 2017-6-16

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评论： Andrew Sundstrom 2017-7-6

I've used Matlab extensively to model biochemical networks with systems of ODEs, though I'm new to using SimBiology. I've imported a calcium channel model into SimBiology and can execute it, plot the results, etc.

What I'd like to do now is take one of the species, Ca — currently with its InitialAmount set to 0.5 millimole/litre, and its BoundaryCondition and ConstantAmount attributes set to on — and control its concentration as a function of time, treating it as an input function to the rest of the system. (I'm investigating how different ways of pulsing Ca concentration will affect downstream production of autonomous CaMKII.)

What is the best way to accomplish building such an input function in SimBiology?

I found this article, which describes how to create a custom user-defined function and use it in reaction, rule, and event expressions. But I don't think this is what I need to do.

I'd appreciate any guidance. Thanks.

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Answer 1

Arthur Goldsipe 2017-6-16

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Hi,

First off, if you want the species to vary over time, then you'll need to set the ConstantAmount property to false.

Next, if you have a function that defines the species value over time, you'll need to use that function in a repeated assignment rule (which is a rule that's evaluated at every time step during the simulation).

SimBiology contains a model of the glucose-insulin response that demonstrates this. The example shows how to switch between simulating a species and using experimentally measure time courses.

-Arthur

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Andrew Sundstrom 2017-7-6

Thank you! Adding a repeated assignment rule solved my problem. Thank you too for the illuminating glucose-insulin response example. Much appreciated. —Andrew

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