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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.* ; Raimundez-Alvarez, E. ; Refisch, L.* ; Rosenblatt, M.* ; Stapor, P. ; Städter, P. ; Wang, D. ; Wieland, F.G.* ; Banga, J.R.* ; Timmer, J.* ; Villaverde, A.F.* ; Sahle, S.* ; Kreutz, C.* ; Hasenauer, J. ; Weindl, D.

PEtab-Interoperable specification of parameter estimation problems in systems biology.

PLoS Comput. Biol. 17:e1008646 (2021)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Markup Language; Exchange; Format
ISSN (print) / ISBN 1553-734X
e-ISSN 1553-7358
Journal PLoS Computational Biology
Quellenangaben Volume: 17, Issue: 1, Pages: , Article Number: e1008646 Supplement: ,
Publisher Public Library of Science (PLoS)
Publishing Place 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Grants National Institute of Health
German Federal Ministry of Education and Research
German Federal Ministry of Economic Affairs and Energy
German Research Foundation
Deutsche Krebshilfe
Human Frontier Science Program
European Union