PEtab-Interoperable specification of parameter estimation problems in systems biology.
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- Record sourced from PubMed, PMID 33497393.
- Also identified by DOI 10.1371/journal.pcbi.1008646 and PMC identifier 7864467.
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Abstract
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.
Medical subject headings
- Programming Languages
- Systems Biology