Awesome
pyPESTO - Parameter EStimation TOolbox for python
<img src="https://raw.githubusercontent.com/ICB-DCM/pyPESTO/master/doc/logo/logo_wordmark.png" width="50%" alt="pyPESTO logo"/>pyPESTO is a widely applicable and highly customizable toolbox for parameter estimation.
Feature overview
pyPESTO features include:
- Multi-start local optimization
- Profile computation
- Result visualization
- Interface to AMICI for efficient simulation and sensitivity analysis of ordinary differential equation (ODE) models (example)
- Parameter estimation pipeline for systems biology problems specified in SBML and PEtab (example)
- Parameter estimation with relative (scaled and offset) data as described in Schmiester et al. (2020). (example)
- Parameter estimation with ordinal data as described in Schmiester et al. (2020) and Schmiester et al. (2021). (example)
- Parameter estimation with censored data. (example)
- Parameter estimation with nonlinear-monotone data. (example)
Quick install
The simplest way to install pyPESTO is via pip:
pip3 install pypesto
More information is available here: https://pypesto.readthedocs.io/en/latest/install.html
Documentation
The documentation is hosted on readthedocs.io: https://pypesto.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 https://pypesto.readthedocs.io/en/latest/contribute.html
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., Lakrisenko, P., Wang, D., Raimúndez, E., Merkt, S., Schmiester, L., Städter, P., Grein, S., Dudkin, E., Doresic, D., Weindl, D., & Hasenauer, J. (2023). pyPESTO: A modular and scalable tool for parameter estimation for dynamic models, Bioinformatics, 2023, btad711, doi:10.1093/bioinformatics/btad711
When presenting work that employs pyPESTO, feel free to use one of the icons in doc/logo/:
<p align="center"> <img src="https://raw.githubusercontent.com/ICB-DCM/pyPESTO/master/doc/logo/logo.png" height="75" alt="AMICI Logo"> </p>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.