consolidate with old template

pull_request_template.md

@@ -1,14 +1,23 @@
-# Checklist for the submission of new problems
-- [ ] The PEtab problem is valid (check with e.g. `petablint -vy problem.yaml`)
-- The problem is setup to quickly reproduce figures from the original paper, by including
-  - [ ] A PEtab visualization file
-  - [ ] Simulated data generated by simulating the PEtab problem with parameters from the original paper
-- [ ] The problem name follows the following convention: `{LAST_NAME_OF_FIRST_AUTHOR}_{ABBREVIATED_JOURNAL_NAME}{YEAR_OF_PUBLICATION}`
+**Checklist for the submission of new PEtab problems**
+- [ ] The problem ID is in the format `{LAST_NAME_OF_FIRST_AUTHOR}_{ABBREVIATED_JOURNAL_NAME}{YEAR_OF_PUBLICATION}`
+- [ ] There is a GitHub issue for this problem
+  - [ ] The problem ID is in the 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
+- [ ] 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 PEtab problem is based on a model that is
   - [ ] peer-reviewed and
   - [ ] published
-- [ ] The model ID and model name attributes in the SBML model file match the problem name
-- [ ] Any information related to methods used with the PEtab problem to reproduce work from the original paper is included in the PR, e.g.:
-  - [ ] Optimization method and hyperparameters
-- [ ] There is an identifier tag to contains a reference to the original publication
 - [ ] 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)