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PEtab-dev / PEtab

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
https://petab.readthedocs.io
MIT License
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Allow using observables in noiseFormula #543

Open dweindl opened 2 years ago

dweindl commented 2 years ago

Currently it is not allowed to use observable IDs in noiseFormula in the observables table (#368). It would be great to allow that.

This would convenient for specifying relative errors. Although the observableFormula could be copied to the noiseFormula, it would be more readable and less error prone if one could simply use the respective observableId.

Also, some tools do not support state variables, but only observables in noise models, so this would be convenient there too.

Opinions?

eraimundez commented 1 year ago

There seems to be something around that maybe could be used / adapted? https://help.juliahub.com/pumasqsp/dev/example/petabimport/ (see first green box when scrolling down)

dweindl commented 1 year ago

There seems to be something around that maybe could be used / adapted? https://help.juliahub.com/pumasqsp/dev/example/petabimport/ (see first green box when scrolling down)

This doesn't really require much adaptation. It's mostly about making a decision whether we want to allow that. (I think we should.) Thanks for the reminder, I'll bring that up again in the next PEtab editor meeting (ping @PEtab-dev/petab-editors).