PEtab-dev / PEtab-dev/PEtab

Specification for formula format

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#522 1 comment 3 reactions 0 assignees View on GitHub

A pull request for this has already been merged.

  • #579 by @dweindl — merged
specification change v1
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Description

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.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by comparing the requested PEtab formula rules with the SBML L3 formula specification and the reported SymPy interpretation of beta and gamma. Define acceptable symbols and functions, including how names such as beta are treated, then verify that the specification gives different PEtab tools a consistent interpretation.

Written by the indexing model from the issue text.

Assessment

Domain
data, documentation
Issue type
Documentation
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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