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PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems

Parameter estimation is a cornerstone of data-driven modeling in systems biology. Yet, constructing such problems in a reproducible and accessible manner remains challenging. The PEtab format has established itself as a powerful community standard to encode parameter estimation problems, promoting i...

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Bibliographic Details
Main Authors: Jost, Paul (Author) , Bergmann, Frank T. (Author) , Weindl, Daniel (Author) , Hasenauer, Jan (Author)
Format: Article (Journal)
Language:English
Published: March 2026
In: Bioinformatics
Year: 2026, Volume: 42, Issue: 3, Pages: 1-4
ISSN:1367-4811
DOI:10.1093/bioinformatics/btag106
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.1093/bioinformatics/btag106
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Author Notes:Paul J. Jost, Frank T. Bergmann, Daniel Weindl, Jan Hasenauer
Description
Summary:Parameter estimation is a cornerstone of data-driven modeling in systems biology. Yet, constructing such problems in a reproducible and accessible manner remains challenging. The PEtab format has established itself as a powerful community standard to encode parameter estimation problems, promoting interoperability and reusability. However, its reliance on multiple interlinked files—often edited manually—can introduce inconsistencies, and new users often struggle to navigate them. Here, we present PEtab-GUI, an open-source Python application designed to streamline the creation, editing, and validation of PEtab problems through an intuitive graphical user interface. PEtab-GUI integrates all PEtab components, including SBML models and tabular files, into a single environment with live error checking and customizable defaults. Interactive visualization and simulation capabilities enable users to inspect the relationship between the model and the data. PEtab-GUI lowers the barrier to entry for specifying standardized parameter estimation problems, making dynamic modeling more accessible, especially in educational and interdisciplinary settings.PEtab-GUI is implemented in Python, open-source under a 3-Clause BSD license. The code, designed to be modular and extensible, is hosted on https://github.com/PEtab-dev/PEtab-GUI, available as a Zenodo repository at https://doi.org/10.5281/zenodo.15355752, and can be installed from PyPI.
Item Description:Veröffentlicht: 05. März 2026
Gesehen am 29.04.2026
Physical Description:Online Resource
ISSN:1367-4811
DOI:10.1093/bioinformatics/btag106

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