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Compartment Models in SBML [message #1408518]

Fri, 15 August 2014 09:02

Christian Thoens

Messages: 2
Registered: January 2012

Junior Member

Here is the simple SIR model in SBML. I created it with COPASI (www.copasi.org). COPASI can also be used to integrate the equation, create a graph or find the steady state. And it has optimization algorithms like Nelder-Mead and Levenberg-Marquard, but I still have to figure out how to use them.

The SBML standard has an entity "Compartment", but in the example S, I and R are implemented as "Species" and not as "Compartment". That's because in COPASI I was able to define transitions between species but I do not find a way to do it between Compartments.

Attachment: SIR.xml
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