pyPESTO - Parameter EStimation TOolbox for python

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 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

References

PESTO: Parameter estimation toolbox for MATLAB. Development is discontinued, but PESTO comes with additional features waiting to be ported to pyPESTO.