Automating Simulation and Scripting for reaction model

[Breveruos Sh]

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.

Breveruos

[Frank Bergmann]

Hello Breveruos, 

Maybe you could have a look at:

* CoRC: https://jpahle.github.io/CoRC/ for high level scripting in R or

* bascio: https://basico.readthedocs.io 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, 

best

Frank