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All Projects → ICB-DCM → pyPESTO

ICB-DCM / pyPESTO

Licence: BSD-3-Clause License
python Parameter EStimation TOolbox

Programming Languages

python
139335 projects - #7 most used programming language

Labels

optimizationsystems-biologyparameter-estimationhacktoberfest

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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 qualitative data as described in Schmiester et al. (2020). This is currently implemented in the feature_ordinal branch.

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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