Work with ODE model system in Simbiology

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Silvia  Casillas
Silvia Casillas on 23 Nov 2021
Commented: Silvia Casillas on 24 Nov 2021
I don't know if my question is a bit silly but, I have a model of a biological system and I have already all the ODEs of the system, but I want to use Simbiology to simulate them to get also an sensibility analysis, the problem is that I don't know if there is a way to work with these ODEs directly in Simbiology or how I have to process the model to get another representation.
As an example I have the equations:
dCd/dt = a1*GF-sd*CD
dR/dt= -k1*R*E+k-1*RE-piu*CD*R
...

Answers (1)

Arthur Goldsipe
Arthur Goldsipe on 23 Nov 2021
Not silly at all. That's a pretty common question. The easiest and most direct way to convert such a model over to SimBiology is to convert each differential equation to a rate rule. You can find an example of that here.
It's more work, but another option is to reconstruct the network of reaction from the differential equations. That's what I prefer to do, sicne it allows me to build a graphical diagram of the reaction network. It can often be less error prone, since SimBiology does more of the bookkeeping for me. We've considered adding a feature to automatically convert rate rules into equivalent reactions, but that hasn't been implemented yet. But this is a good point of imformation as we prioritize what to work on next.
-Arthur

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