Automating Simulation and Scripting for reaction model

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Breveruos Sh

May 11, 2024, 1:17:51 PMMay 11
to COPASI User Forum

I'm seeking guidance on simulation automation and scripting. I need to find a convenient method to script,  see "Specifically".

Copasi doesn't have a built-in scripting tool as far as I know.

There are two API methods available: the C++ API and the Copasi API. However, as someone without a software background, I find myself at a loss on where to begin.

I am familiar with using MATLAB, so I attempted to convert the C code to MATLAB. However, I found this process challenging, especially when my model changes and requires conversion again.

I also tried importing SBML into MATLAB but wasn't sure what to focus on exactly.

"Specifically", I have a model with 240 reactions and 90 states. For this model, I want to run a large number of sets of fixed parameters (inputs) and use an optimization function, like particle swarm, to find the best variable parameters (outputs) for each set.

Additional information: I built my model using COPASI 4.4 on Windows.


Frank Bergmann

May 11, 2024, 1:59:44 PMMay 11
to COPASI User Forum
Hello Breveruos, 

Maybe you could have a look at:

* CoRC: for high level scripting in R or
* bascio: for high level scripting in python 

Another way would be to mark the optimisation task as scheduled, and have versions of it for each parameter set separately solved on a cluster environment using CopasiSE. 

let us know if you need additional help, 

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