User Guide

  • PEtab-GUI
    • Installation
      • From PyPI
      • From GitHub
      • From a local copy
    • Usage
      • Examples
    • Features
  • PEtab-GUI Tutorial
    • Introduction
    • Getting Started
      • Installation
      • Launching the Application
    • The Main Window
    • Quick Start: Your First PEtab Problem
      • Step 1: Launch PEtab-GUI
      • Step 2: Create the SBML Model
      • Step 3: Import Measurement Data
      • Step 4: Define the Observable Formulas
      • Step 5: Review Auto-Generated Conditions
      • Step 6: Configure Parameters for Estimation
      • Step 7: Visualize Your Measurements
      • Step 8: Run a Simulation
      • Step 9: Save Your Project
      • Congratulations!
    • Opening an Existing PEtab Problem
    • Creating/Editing a PEtab Problem
      • Creating/Editing an SBML Model
      • Specifying Measurements
      • Importing Matrix-Format Measurement Data
        • Understanding Matrix Format
        • Step-by-Step: Importing Matrix Data
        • Common Matrix Import Scenarios
        • Troubleshooting Matrix Import
        • Tips for Successful Matrix Import
      • Defining Observables
      • Setting Up Experimental Conditions
      • Setting Up Parameters
    • Validation and Inspection
      • Visualization and Simulation
      • Linting
    • Advanced Features
      • Filtering
      • Find and Replace
      • Multi-Cell Editing
      • Help Mode / Tutorial Mode
      • Customizable Table Layout
      • Undo and Redo
      • Recent Files
    • Saving Your Project
    • Additional Resources
  • Next Steps
    • Parameter Estimation with pyPESTO
    • Model Simulation with AMICI
    • Model Simulation with COPASI
    • Parameter Estimation with PEtab.jl
    • Parameter Estimation with Data2Dynamics
    • Contribute to the Benchmark Collection
    • Additional Resources

Development

  • GitHub Repository
  • Contributing
    • Development Setup
    • Building the documentation
    • Filing an Issue
PEtab-GUI
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© Copyright 2025, Paul Jonas Jost, Frank T. Bergmann.

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