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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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Specification for formula format #522

Open dilpath opened 3 years ago

dilpath commented 3 years ago

Which problem would you like to address? Please describe. Lack of specification of the format for formulae (e.g. observable/noise formulae) in PEtab tables.

Describe the solution you would like A specification that clarifies acceptable/unacceptable (usage of) symbols (e.g. accepted functions).

Describe alternatives you have considered One possibility is to use the specification for SBML L3 formulae.

Additional context The current issue is that many published models use e.g. beta and gamma as parameter IDs, but SymPy interprets these as the Beta and Gamma functions, resulting in linting errors in libpetab-python.

Don't mind what the specification is in the end (e.g. whether beta is considered a function or model component), since it's easy enough to e.g. rename beta to beta_. The point of the specification would be for consistency in the interpretation of formulae between different PEtab tools.

dweindl commented 2 years ago

Agreed that this would be very important to specify.

This might serve as a good starting point http://sbml.org/Special/Software/libSBML/docs/formatted/python-api/libsbml-math.html, but other suggestions are welcome.

Happy about any pull request to clarify this in the PEtab documentation.