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Benchmark-Models-PEtab

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. The publication for the introduction and analysis of the benchmark problem collection is available at https://academic.oup.com/bioinformatics/article/35/17/3073/5280731.

Contributions to the collection are very welcome. Please see CONTRIBUTING.md for more details.

Overview

PEtab Problem ID	Conditions	Estimated Parameters	Events	Preequilibration	Postequilibration	Measurements	Observables	Noise distribution(s)	Species	References	SBML4Humans
Alkan_SciSignal2018	73	56	0	0	0	1733	12	normal	36	[1]	[1]
Bachmann_MSB2011	36	113	0	0	0	541	20	normal; log10-normal	25	[1]	[1]
Beer_MolBioSystems2014	19	72	0	0	0	27132	2	normal	4	[1]	[1]
Bertozzi_PNAS2020	2	8	0	0	0	22	2	normal	3	[1]	[1]
Blasi_CellSystems2016	1	9	0	0	1	252	15	log-normal	16	[1]	[1]
Boehm_JProteomeRes2014	1	9	0	0	0	48	3	normal	8	[1]	[1]
Borghans_BiophysChem1997	1	23	0	0	0	111	1	log10-normal	3	[1]	[1]
Brannmark_JBC2010	8	22	0	1	0	43	3	normal	9	[1]	[1]
Bruno_JExpBot2016	6	13	0	0	0	77	5	normal	7	[1]	[1]
Chen_MSB2009	4	155	0	0	0	120	3	normal	500	[1]	[1]
Crauste_CellSystems2017	1	12	0	0	0	21	4	normal	5	[1]	[1]
Elowitz_Nature2000	1	21	0	0	0	58	1	log10-normal	8	[1]	[1]
Fiedler_BMC2016	3	22	0	0	0	72	2	normal	6	[1]	[1]
Froehlich_CellSystems2018	9169	4231	0	0	9169	9169	1	normal	1396	[1]	[1]
Fujita_SciSignal2010	6	19	0	0	0	144	3	normal	9	[1]	[1]
Giordano_Nature2020	1	50	0	0	0	313	7	normal	13	[1]	[1]
Isensee_JCB2018	123	46	0	1	0	687	3	normal	25	[1]	[1]
Lang_PLOSComputBiol2024	1	294	0	0	0	9600	16	normal	124	[1]	[1]
Laske_PLOSComputBiol2019	3	13	0	0	0	42	13	normal; log-normal	41	[1] [2] [3]	[1]
Lucarelli_CellSystems2018	16	84	0	0	0	1755	65	normal; log10-normal	33	[1]	[1]
Okuonghae_ChaosSolitonsFractals2020	1	16	0	0	0	92	2	normal	9	[1]	[1]
Oliveira_NatCommun2021	1	12	0	0	0	120	2	normal	9	[1]	[1]
Perelson_Science1996	1	3	0	0	0	16	1	log10-normal	4	[1]	[1]
Rahman_MBS2016	1	9	0	0	0	23	1	normal	7	[1]	[1]
Raia_CancerResearch2011	4	39	0	0	0	205	8	normal	14	[1]	[1]
Raimundez_PCB2020	170	136	0	4	0	627	79	normal	22	[1]	[1]
SalazarCavazos_MBoC2020	4	6	0	0	0	18	3	normal	75	[1]	[1]
Schwen_PONE2014	19	30	0	0	0	286	4	log10-normal	11	[1]	[1]
Smith_BMCSystBiol2013	35	25	3	0	0	62	9	normal	133	[1]	[1]
Sneyd_PNAS2002	9	15	0	0	0	135	1	normal	6	[1]	[1]
Weber_BMC2015	2	36	0	1	0	135	8	normal	7	[1]	[1]
Zhao_QuantBiol2020	7	28	0	0	0	82	1	normal	5	[1]	[1]
Zheng_PNAS2012	1	46	0	1	0	60	15	normal	15	[1]	[1]

License

Any original content in this repository may be used under the terms of the BSD-3-Clause license. Different terms may apply to models and datasets, for which we refer the user to the original publications that are referenced in the respective SBML files.

Installation

See INSTALL.md.

How to Cite

When using this work, please cite an appropriate version on Zenodo: https://doi.org/10.5281/zenodo.8155057

References

The model collection has been used in multiple publications.

If you used the benchmark problems in your work and your publication is missing, please let us know via a new GitHub issue.