Dilan Pathirana
Dilan Pathirana
**What did you expect to happen?** A PEtab parameter with `estimate=0` is treated as a fixed parameter during import. The parameter is defined in the PEtab parameters table, then the...
**What did you expect to happen?** Sensitivities to be computed **What has happened instead?** `rdata.x` and `rdata.sx` are zero matrices **To Reproduce** Compile a model with algebraic expressions, e.g. SBML...
related: #16 #540 If you are already familiar with this, you could skip straight to the "Feedback" section and share your thoughts. A couple of (currently unofficial) PEtab extensions have...
**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...
- [ ] move repo to `PEtab-dev` org - [ ] rename repo `benchmark-problems` (i.e. `PEtab-dev/benchmark-problems`) - [ ] rename `Benchmark-Models` directory to `problem` (i.e. `PEtab-dev/benchmark-problems/problems`) - [ ] add...
Reported by @plakrisenko The measurements and simulation are almost identical. Comparing the data [1] and simulation [2] from the original benchmark collection. - [1] seems to correspond with the data...
- [ ] Bachmann_MSB2011 - [ ] Beer_MolBioSystems2014 - [ ] Blasi_CellSystems2016 - [ ] Borghans_BiophysChem1997 - [ ] Brannmark_JBC2010 - [ ] Crauste_CellSystems2017 - [ ] Elowitz_Nature2000 - [...
Currently varies, with values like `COPASI0`, `arFramework3`, or the model name. Seen in #153 Possible options: - the model name - `benchmark_models_petab` `metaid` and annotation attributes are described in the...