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Checklist for new submissions (#206)
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dilpath authored Apr 18, 2024
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14 changes: 0 additions & 14 deletions .github/PULL_REQUEST_TEMPLATE/new_petab_problem.md

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22 changes: 22 additions & 0 deletions .github/PULL_REQUEST_TEMPLATE/pull_request_template.md
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**Checklist for the submission of new PEtab problems**
- [ ] The PEtab problem is based on a model that is peer-reviewed and published
- [ ] The problem ID is in the format `{LAST_NAME_OF_FIRST_AUTHOR}_{ABBREVIATED_JOURNAL_NAME}{YEAR_OF_PUBLICATION}`
- [ ] The problem ID is in the pull request title
- [ ] There is a GitHub issue for this problem
- [ ] The problem ID is in the issue title
- [ ] A brief model description (one or two sentences)
- [ ] A brief data description (one or two sentences)
- [ ] The issue and PR are linked to each other
- [ ] Differences between the implementation and the original publication are described
- [ ] Experience of fitting / uncertainty analysis (e.g. optimizer used, hyperparameters, reproducibility of best fit)
- [ ] Source of nominal parameters (e.g.: taken from the original publication, or from your own fitting)
- [ ] The SBML file
- [ ] Annotation with reference to the original publication ([example](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/3154d27edbfc4eb19b768465945bc81381a7c964/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml#L4-L14))
- [ ] The model ID and model name attributes in the SBML model file match the problem name ([example](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/3154d27edbfc4eb19b768465945bc81381a7c964/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml#L3))
- [ ] PEtab files
- [ ] A "simulated data" measurement table is included, using the nominal parameters
- [ ] A visualization table is included, that can be used with the simulate data to reproduce figures from the original publication
- [ ] The PEtab problem is valid (check with e.g. `petablint -vy problem.yaml`)
- [ ] The PEtab problem author(s) are assigned to the GitHub issue
- [ ] The README has been updated with `python scripts/overview.py --update`
- [ ] The new PEtab problem row in the generated table has the correct reference (and other entries)
1 change: 1 addition & 0 deletions CONTRIBUTING.md
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New submissions are very welcome! Please check our [pull request template](.github/PULL_REQUEST_TEMPLATE/pull_request_template.md) for guidelines.

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