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

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.

Answer 1

[Arthur Goldsipe]

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

[Andrew Sundstrom]

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

[Ji]

Hi,

Same question as in the orignal post. Is there a way to define a species like a step fucntion so that it increases to a constant after a specific time point in the design app? I tried to use 'events' to trigger a species increase after a time piont, but the species is not a constant and changed during reactions. I also tried 'dose', which behaved almost same as 'event' triggered species increase.

Thank you very much!

-Ji

[Jeremy Huard]

Hi @Ji,

do you mean that the species you would like to increase stepwise should be involved in reactions but its concentration should be stepwise constant?

If this is the case, you can se the BoundaryCondition property of this species to true. This will ensure that the reactions do not affect the dynamics of the species.

Best,

Jérémy

[Ji]

Thank you very much Jeremy!