python-based Parameter EStimation TOolbox
Project description
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 qualitative data as described in
Schmiester et al. (2019).
This is currently implemented in the
feature_ordinalbranch.
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.
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