Possible to upload sets of parameters from a *.csv file (or some such other flat format) to a COPASI model?

[Ben G Small]

Hi.

I just wanted to ask whether it's possible to upload a set of parameters into a COPASI model file? preferably from a flat file format (like *.csv)?

Thanks and regards

Ben

[Frank Bergmann]

We don't have export for loading csv files directly. However, we do support to export the parameters of a COPASI model to file from the command line using CopasiSE. For example

CopasiSE --exportIni params.ini brusselator.cps

would export the parameters of the brusselator.cps file into a params.ini text file. 

This format can also be used to load the parameters back in. For example: 

CopasiSE --reparameterize params.ini -s brusselator-out.cps  brusselator.cps

This would load the 'brusselator.cps' file, apply the parameter changes from params.ini and save the resulting model as 'brusselator-out.cps'. (Note that we just discovered a bug that this currently does not change initial concentrations, but that will be fixed soon). 

If you need something more flexible, your best chance is using some simple scripting using either 

* corc: https://jpahle.github.io/CoRC/articles/CoRC.html or 

* basico: https://basico.readthedocs.io/en/latest/

I hope this helps, 

best

Frank

[Ben G Small]

Dear Frank

Thanks for your reply, as an R user - I'll try CoRC.

Thanks!

Ben

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