Benchmark-Models-PEtab

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Add Heldt et al. (2012)

2

https://www.ncbi.nlm.nih.gov/pubmed/22593159 SBML: https://www.ebi.ac.uk/biomodels/BIOMD0000000463 Estimated complexity of implementation: low

JanHasenauer

Issues with Crauste Model

2

I just had a brief look at the model equations to investigate sources of the notorious integration issues with that model and ... I am not necessarily surprised that this...

FFroehlich

new format for swameye

6

LoosC

Millard P, Smallbone K, Mendes P (2017) Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PLOS Computational Biology...

dweindl

Zheng_PNAS2012: measurements matches simulation

1

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...

dilpath

Errors in Chen_MSB2009 benchmark

4

Looking at the Chen_MSB2009 benchmark model, I suspect I may have identified some errors in the measurements table (https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/master/Benchmark-Models/Chen_MSB2009/measurementData_Chen_MSB2009.tsv). The original data is available from the supplement of https://doi.org/10.1038/msb.2008.74 (MSB...

FFroehlich

**Publication details**: **Title**: A biochemical necroptosis model explains cell type-specific responses to cell-death cues **Reference**: https://doi.org/10.1016/j.bpj.2023.01.035 **Code and model availability**: https://pysb.org/ Python Model available at https://github.com/LoLab-MSM/NERM **Experimental data**: Data available...

C-Peiter

Publication is in Nature Medicine, not Nature as far as I can tell: https://www.nature.com/articles/s41591-020-0883-7

FFroehlich

Machine readable model property overview

2

Would be nice to have the table provided in README.md in some machine readable format like `.csv` or `.tsv`.

FFroehlich

Add CITATION.cff

1

Would be good to have a [CITATION.cff](https://citation-file-format.github.io/), showing how the benchmark collection is to be cited.

dweindl