Benchmark-Models-PEtab

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**Publication details:** - Title: _Thermodynamically consistent model calibration in chemical kinetics_ **Reference:** - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117730/pdf/1752-0509-5-64.pdf **Code and model availability:** - http://www.sbtoolbox2.org/main.php - MATLAB - SBML files found in [Biomodels DB](https://www.ebi.ac.uk/biomodels/BIOMD0000000399) **Experimental...

stephanmg

**Publication details:** - Title: _In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis_ **Reference:** - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4062111/pdf/1752-0509-8-54.pdf **Code and model availability:** - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4062111/bin/1752-0509-8-54-S2.xml - COPASI - SBML...

stephanmg

https://www.embopress.org/doi/full/10.1038/msb.2013.19 SBML model: https://www.ebi.ac.uk/biomodels/BIOMD0000000482 Complexity: medium

JanHasenauer

Finish Merkle model

1

Model is rather complicated and has not been worked on yet. Maybe try D2D export?

LeonardSchmiester

https://www.frontiersin.org/articles/10.3389/fmicb.2020.00725/full The code is not publicly available, but they write it is made available upon request. D2D was used, so might be easy to implement the model using the D2D...

LeonardSchmiester

https://www.nature.com/articles/s41598-021-82215-2

LeonardSchmiester

Add new model Raimúndez et al. (2021)

4

https://www.medrxiv.org/content/10.1101/2020.04.19.20071597v1

LeonardSchmiester

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008421

LeonardSchmiester

https://www.embopress.org/doi/10.15252/msb.20198955

LeonardSchmiester

Write function to generate benchmark_model_characteristics.xlsx automatically

4

Most of the fields are very easy to fill. We simply need the bibtex files for the models in the respective folders and (optional) also a remark file (in case...

JanHasenauer