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PEtab is a data format for specifying parameter estimation problems insystems biology. This repository contains the PEtab specifications andadditional documentation.

PEtab is built aroundSBML and based on tab-separated values(TSV) files. It is meant as a standardized way to provide information forparameter estimation, which is out of the current scope of SBML. This includes,for example:

• Specifying and linking measurements to models

  • Defining model outputs

  • Specifying noise models

• Specifying parameter bounds for optimization

• Specifying multiple simulation conditions with potentially shared parameters

Documentation of the PEtab data format is available athttps://petab.readthedocs.io/en/latest/.

To participate in PEtab editor elections, discussions on new PEtabdevelopments, or PEtab-related events, please join ourpetab-discuss mailing list.

Any contributions and feedback to PEtab are very welcome, see ourcontribution guide.

A wide range of PEtab examples can be found in the systems biology parameter estimationbenchmark problem collection.

For a list of tools supporting PEtab, see thesoftware support page.

If you would like to use PEtab yourself, please have a look at:

• a PEtab tutorialgoing through the individual steps of setting up a parameter estimationproblem in PEtab, independently of any specific software
• the PEtab format reference
• the example models provided in thebenchmark collection.
• the tutorials provided with each of the softwares supporting PEtab

To convert your existing parameter estimation problem to the PEtab format, youwill have to:

1. Specify your model in SBML.

2. Create a condition table.

3. Create a table of observables.

4. Create a table of measurements.

5. Create a parameter table.

6. Create a YAML file that lists the model and all of the tables above.

If you are using Python, some handy functions of thePEtab library can helpyou with that. This includes also a PEtab validator calledpetablint whichyou can use to check if your files adhere to the PEtab standard. If you havefurther questions regarding PEtab, feel free to post anissue at our GitHub repository.

PEtab files can be created or edited using any text editor or spreadsheetsoftware, or programmatically (see libraries below).There is also a dedicated graphical user interface for creating and editingPEtab 1.0 files, calledPEtab-GUI.

PEtab comes with a Python package for creating, checking, visualizing andworking with PEtab files. This package is available athttps://github.com/PEtab-dev/libpetab-python/.

There is also an R package for PEtab in development, which currently supports:consistent manipulation of experimental conditions, measurements, andobservables; and visualizing measurements. It also provides an interface to thePEtab Python library, and an interface to dMod that supports: conversion ofdMod models to SBML; and simulation and visualization of results. The packageis available athttps://github.com/dlill/petab/.

Other standardization-related projects that extend or build on PEtab include:

• PEtab SelectPEtab Select brings model selection to PEtab. It comprises both astandardized way to define model selection problems in PEtab and a Pythonlibrary to work with these problems.

• petabunit (WIP)A Python library that extends PEtab to annotate and convert physical units.

• PEtab SciML (WIP)PEtab SciML brings Scientific Machine Learning (SciML) models thatcombine mechanistic and machine learning models to PEtab. It comprisesboth a standardized way to define SciML problems, and a Python libraryto work with these problems.

If you have any questions or problems with PEtab, feel free to post them atour GitHubissue tracker.