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DOI

PEtabGUI

PEtabGUI provides a graphical user interface to inspect and edit parameter estimation problems encoded in the PEtab format.

Installation

From PyPI

To install PEtabGUI from PyPI, run:

pip install petab_gui

From GitHub

To install the latest development version from GitHub, run:

    pip3 install git+https://github.com/PaulJonasJost/PEtab_GUI/

From a local copy

  1. Clone the repository:

    git clone https://github.com/PaulJonasJost/PEtab_GUI.git

  2. Install the package from the root of the working tree:

    pip install .

Usage

After installation, launch the PEtab GUI from the command line using the petab_gui command.

Optionally, you can provide the path to an existing PEtab YAML file as an argument.

Features

The PEtabGUI provides a Python-based graphical user interface that simplifies the creation, editing, and validation of PEtab parameter estimation problems.

  • Unified Environment
    • Integrates all PEtab components (SBML/PySB models, conditions, observables, measurements, parameters, and visualization files).
    • Supports drag-and-drop import of YAML or individual component files.
    • Automatically resolves mismatches and converts matrix-format experimental data into valid PEtab format.
  • Interactive and Intuitive Editing
    • Dockable, resizable, and movable table widgets for each PEtab file.
    • Context-aware editing with combo-boxes, drop-downs, and multi-cell editing.
    • Automatic generation of missing observables/conditions with customizable defaults.
    • Real-time validation and plausibility checks with PEtab linting tools.
    • SBML view in both XML and human-readable Antimony syntax.
  • Visualization and Simulation
    • Interactive plots linking measurement data with model simulations.
    • Bidirectional highlighting between plots and tables.
    • Built-in simulation via BasiCO with one-click parameter testing.
    • Intelligent defaults for visualization with optional user customization.
    • Ability to disable plotting for large models to maintain responsiveness.
  • Archiving and Export
    • Export individual tables, the SBML model, or complete PEtab problems.
    • Save as directory structures or COMBINE archives for reproducibility