Benchmark-Models-PEtab

Benchmark-Models-PEtab copied to clipboard

inital, initial https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/8c2290bc47dbb43d2f14e36444dca238db504d9c/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml#L1317

dweindl

Currently, the "events" column of the overview table only shows actual SBML events. I'd say it should also count `piecewise`. E.g., Giordano_Nature2020 does not have any SBML events, but a...

dweindl

Check/fix tsv files to enable preview

1

GitHub offers a nice tsv table preview, but this only works for well-behaved files. For example, all rows need to have the same number of columns. This is not always...

dweindl

**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...

m-philipps

Add Liu_IFACPapersOnLine2025

4

Yuhong's publication on oncolyte virus therapy in zebrafish has a model in PEtab format, at the moment in the preprint phase.

m-philipps

Include objective function values and gradients at nominal parameter values

4

As mentioned in https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/issues/208, I think the relevance of this repository could be increased further, by including objective function values and gradients at the provided nominal parameter values, supporting its...

dweindl

Add reformulated Fiedler_BMCSystBiol2016

1

The authors used an identifiable, reformulated version of the model for Raf/MEK/ERK signaling after release from S-phase arrest: > The model for the relative phosphorylation levels does not depend explicitly...

m-philipps

Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting https://www.embopress.org/doi/full/10.1038/s44320-024-00073-2

m-philipps

Isensee_JCB2018: fix SBML parameter values

2

In #132, this problem was changed to remove model selection parameters (if they were not selected). All model selection parameters in the SBML model were also set to 0. This...

dilpath

**Checklist for the submission of new PEtab problems** - [x] The PEtab problem is based on a model that is peer-reviewed and published - [x] The problem ID is in...

mariesieger