PEtab—Interoperable specification of parameter estimation problems in systems biology
Open accessAbstract
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been—so far—no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.
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The lack of a standardized format for parameter estimation makes it difficult to switch between tools, hindering reproducibility.
“The lack of a standardized format makes it difficult to switch between tools, hindering reproducibility [51].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [51]
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- Authors
- Schmiester, L., Schälte, Y., Bergmann, F. T., Camba, T., Dudkin, E., Egert, J., Fröhlich, F., Fuhrmann, L., Hauber, A. L., Kemmer, S., Lakrisenko, P., Loos, C., Merkt, S., Müller, W., Pathirana, D., Raimúndez, E., Refisch, L., Rosenblatt, M., Stapor, P. L., Städter, P., Wang, D., Wieland, F.-G., Banga, J. R., Timmer, J., Villaverde, A. F., Sahle, S., Kreutz, C., Hasenauer, J., & Weindl, D.
- Affiliations
- Helmholtz Munich (DE)
- Heidelberg University (DE)
- Consejo Superior de Investigaciones Científicas (ES)
- University of Bonn (DE)
- University of Freiburg (DE)
- Harvard University (US)
- Ragon Institute of MGH, MIT and Harvard (US)
- Heidelberg Institute for Theoretical Studies (DE)
- Corresponding author
- Hasenauer, Jan
- ORCID
- Schmiester, Leonard
- Schälte, Yannik
- Bergmann, Frank T.
- Dudkin, Erika
- Egert, Janine
- Fröhlich, Fabian
- Fuhrmann, Lara
- Hauber, Adrian L.
- Kemmer, Svenja
- Lakrisenko, Polina
- Loos, Carolin
- Merkt, Simon
- Müller, Wolfgang
- Pathirana, Dilan
- Raimúndez, Elba
- Refisch, Lukas
- Rosenblatt, Marcus
- Stapor, Paul L.
- Städter, Philipp
- Wang, Dantong
- Wieland, Franz-Georg
- Banga, Julio R.
- Timmer, Jens
- Villaverde, Alejandro F.
- Sahle, Sven
- Kreutz, Clemens
- Hasenauer, Jan
- Weindl, Daniel
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2021-01-26
- Volume
- 17
- Issue
- 1
- Pages
- e1008646
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC7864467
- OpenAlex
- W3014365047
- Cited by
- 96
- References
- 26
- Citations by year
- 2026: 20 · 2025: 14 · 2024: 20 · 2023: 14 · 2022: 17 · 2021: 8 · 2020: 3
- FWCI
- 4.63
- Type
- journal article
- Language
- en
- Update notices
- new_version (2021-02-05)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Investigo Institutional repository of UVigo (Universidade de Vigo) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- mediaTUM (Technical University of Munich) (submittedVersion, other-oa)
- Site cant be reached (submittedVersion, cc-by)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion, cc-by)
- arXiv (Cornell University) (cc-by)
- Figshare (cc-by)
- Funders
- European Commission (HORIZON2020, EXC 2151, 686282)
- Deutsche Forschungsgemeinschaft (CIBSS-EXC 2189, 031L0048, EXC‐2189, HA7376/1-1, 70112355, EXC 2151, 390939984, 272983813, EXC-2047, 01ZX1310B, 686282, TRR179)
- Bundesministerium für Bildung und Forschung (031L0104A, de.NBI ModSim1, 01ZX1705A, 01ZX1916A, EXC-2189, 390939984, 01ZX1310B, 031L0080, 031L0048, 031L0159C, 70112355)
- Deutsche Krebshilfe (390939984, 031L0048, 70112355, EXC-2189)
- German Network for Bioinformatics Infrastructure
- National Cancer Institute (U54CA225088)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- PEtab, parameter estimation, systems biology, SBML, interoperability, reproducibility, data-driven modeling, observation model, experimental data, Python library
- MeSH terms
- Algorithms, Models, Biological, Programming Languages, Reproducibility of Results, Models, Statistical, Databases, Factual, Systems Biology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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