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python-based Parameter EStimation TOolbox

Project description

pyPESTO - Parameter EStimation TOolbox for python

pyPESTO logo

pyPESTO is a widely applicable and highly customizable toolbox for parameter estimation.

PyPI CI Coverage Documentation DOI

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 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:


The documentation is hosted on


Multiple use cases are discussed in the documentation. In particular, there are jupyter notebooks in the doc/example directory.


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: DOI

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/:


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.


pyPESTO supersedes PESTO a parameter estimation toolbox for MATLAB, whose development is discontinued.

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pypesto-0.5.1.tar.gz (314.3 kB view hashes)

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