PEtab-GUI: A graphical user interface to create, edit and inspect PEtab parameter estimation problems
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arXiv
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| Main Authors: | , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866908653700775936 |
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| author | Jost, Paul Jonas Bergmann, Frank T Weindl, Daniel Hasenauer, Jan |
| author_facet | Jost, Paul Jonas Bergmann, Frank T Weindl, Daniel Hasenauer, Jan |
| contents | Motivation: 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.
Availability and Implementation: 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 and can be installed from PyPI.
Key words: Parameter Estimation, Python, Graphical User Interface, Systems Biology |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2511_11515 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | PEtab-GUI: A graphical user interface to create, edit and inspect PEtab parameter estimation problems Jost, Paul Jonas Bergmann, Frank T Weindl, Daniel Hasenauer, Jan Quantitative Methods Motivation: 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. Availability and Implementation: 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 and can be installed from PyPI. Key words: Parameter Estimation, Python, Graphical User Interface, Systems Biology |
| title | PEtab-GUI: A graphical user interface to create, edit and inspect PEtab parameter estimation problems |
| topic | Quantitative Methods |
| url | https://arxiv.org/abs/2511.11515 |