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

TL;DR

PEtab-GUI is an open-source Python tool that simplifies creating, editing, and validating PEtab parameter estimation problems with an intuitive GUI, enhancing accessibility and reproducibility in systems biology modeling.

Contribution

It introduces a comprehensive graphical interface for PEtab, integrating model components and validation tools to lower barriers for users and improve reproducibility.

Findings

Streamlines creation and editing of PEtab problems

Provides live error-checking and visualization tools

Enhances accessibility for educational and interdisciplinary use

Abstract

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