pyPESTO - Parameter EStimation TOolbox for python
pyPESTO is a widely applicable and highly customizable toolbox for parameter estimation.
Feature overview
Feature overview of pyPESTO. Figure taken from the Bioinformatics publication.
pyPESTO features include:
- Parameter estimation interfacing multiple optimization algorithms including
- Interface to multiple simulators including
- Uncertainty quantification using various methods:
- Complete parameter estimation pipeline for systems biology problems specified in
- Parameter estimation pipelines for different modes of data:
- Model selection. (example)
- Various visualization methods to analyze parameter estimation results.
Quick install
The simplest way to install pyPESTO is via pip:
pip3 install pypestoMore information is available here: https://pypesto.readthedocs.io/en/latest/install.html
Documentation
The documentation is hosted on readthedocs.io:
Examples
Multiple use cases are discussed in the documentation. In particular, there are jupyter notebooks in the doc/example directory.
Contributing
We are happy about any contributions. For more information on how to contribute
to pyPESTO check out
How to Cite
Citeable DOI for the latest pyPESTO release:
When using pyPESTO in your project, please cite
- Schälte, Y., Fröhlich, F., Jost, P. J., Vanhoefer, J., Pathirana, D., Stapor, P.,
When presenting work that employs pyPESTO, feel free to use one of the icons in doc/logo/:
There is a list of publications using pyPESTO. If you used pyPESTO in your work, we are happy to include your project, please let us know via a GitHub issue.
References
pyPESTO supersedes PESTO a parameter estimation toolbox for MATLAB, whose development is discontinued.