petab - a Python package for handling PEtab files

PEtab is a data format for specifying parameter estimation problems in systems biology. This repository provides the petab Python package for reading, writing and validating PEtab files.

Documentation

Documentation of the petab Python package is available at https://libpetab-python.readthedocs.io/en/latest/. Documentation of the PEtab format in general is available at https://petab.readthedocs.io/en/latest/.

Installation

The PEtab library is available on pypi and the easiest way to install it is running

pip3 install petab

It will require Python>=3.9 to run. (We are following the numpy Python support policy).

Development versions of the PEtab library can be installed using

pip3 install https://github.com/PEtab-dev/libpetab-python/archive/develop.zip

(replace develop by the branch or commit you would like to install).

When setting up a new parameter estimation problem, the most useful tools will be:

The PEtab validator, which is automatically installed using Python entrypoints to be available as a shell command from anywhere, called petablint
petab.create_parameter_df to create the parameter table, once you have set up the model, condition table, observable table and measurement table
petab.create_combine_archive to create a COMBINE Archive from PEtab files

Examples

Examples for PEtab Python library usage:

Getting help

If you have any question or problems with this package, feel free to post them at our GitHub issue tracker.

Contributing