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>=3.7.1 to run.
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 now automatically installed using Python entrypoints to be available as a shell command from anywhere called
petablintpetab.create_parameter_dfto create the parameter table, once you have set up the model, condition table, observable table and measurement tablepetab.create_combine_archiveto create a COMBINE Archive from PEtab files
Getting help¶
If you have any question or problems with this package, feel free to post them at our GitHub issue tracker.
Contributing¶
Contributions and feedback to this package are very welcome, see our contribution guide.
Python package
- API Reference
- petab
- petab.composite_problem
- petab.core
- petab.conditions
- petab.C
- petab.lint
- petab.measurements
- petab.parameter_mapping
- petab.parameters
- petab.problem
- petab.sampling
- petab.sbml
- petab.yaml
- petab.visualize.data_overview
- petab.visualize.helper_functions
- petab.visualize.plot_data_and_simulation
- petab.visualize.plotting_config
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