A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
[ ] rename repo to something like PEtab-Benchmark-Collection/PEtab-Benchmark-Problems to better match common usage
[ ] rename Benchmark-Models directory to e.g. Benchmark-Problems or Problems
[ ] add metadata to each problem in its PEtab YAML file (closes #25)
[ ] create schema for such metadata
[ ] include objective function value evaluated at nominal parameters (possibly closes #17 unless that it about curation itself). also optionally the Chi2.
[ ] include DOI to original publication
[ ] copy all relevant metadata from model to PEtab YAML, including e.g. model ID (closes #155)
[ ] create script to automatically extract interesting problem "features" then produce a "problem" vs. "feature" matrix TSV file for convenience (closes #18 #19). example features (maybe difficult to extract): "splines", "log-scale observables", "parameter-dependent initial conditions". Include all features currently in README overview table.
[ ] add check for correctly-formatted simulation tables (closes #20)
PEtab-Benchmark-Collection
/PEtab-Benchmark-Problems
to better match common usageBenchmark-Models
directory to e.g.Benchmark-Problems
orProblems