Add support for non-SBML models
A pull request for this has already been merged.
- #538 by @dweindl — merged
- Dominant language
- No language data
- Stars
- 66
- Forks
- 16
- Avg merge
- 3h 2m
- Merged PRs (30d)
- 10
Description
Would be great if PEtab would be usable with non-SBML models. Formats to consider would include e.g. cellML, bngl, pysb, .... Personally interested in pysb support.
Will be a significant implementation effort, but probably worth it. Need to abstract from model implementation. For preparation, all libsbml.Model instances should be replaced by new class Model, abstract base class. Concrete implementations would be SbmlModel, PysbModel, ...
This does not imply any changes in file formats (yet). For the next format update, it would be good to already think about how to handle that e.g. in yaml files. Allow for sbml_model_file, xx_model_file, ... or add model_type?
Anybody interested in joining in for that?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Review the current uses of libsbml.Model and the merged pull request #538 before starting, then assess how model implementations could be abstracted behind a common Model interface. Done would require a working non-SBML implementation, such as PySB support, without changing file formats yet.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100