python 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
Parameter estimation pipeline for systems biology problems specified in SBML and PEtab

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.

Project details

Release history Release notifications | RSS feed

0.5.4

Oct 31, 2024

0.5.3

Jul 30, 2024

0.5.2

May 31, 2024

0.5.1

Apr 17, 2024

0.5.0

Apr 17, 2024

0.4.2

Apr 15, 2024

0.4.1

Dec 6, 2023

0.4.0

Nov 22, 2023

0.3.3

Oct 20, 2023

0.3.2

Oct 2, 2023

0.3.1

Jun 29, 2023

0.3.0

May 2, 2023

0.2.17

May 2, 2023

0.2.16

Feb 23, 2023

0.2.15

Dec 21, 2022

0.2.14

Nov 9, 2022

0.2.13

Jun 2, 2022

0.2.12

Apr 14, 2022

0.2.11

Jan 12, 2022

0.2.10

Jan 7, 2022

0.2.9

Nov 5, 2021

0.2.8

Oct 28, 2021

0.2.7

Aug 3, 2021

0.2.6

May 17, 2021

0.2.5

May 5, 2021

0.2.4

Mar 17, 2021

0.2.3

Jan 26, 2021

0.2.2

Oct 5, 2020

0.2.1

Sep 7, 2020

0.2.0

Jul 2, 2020

0.1.0

Jun 17, 2020

0.0.13

May 3, 2020

0.0.12

Apr 6, 2020

0.0.11

Mar 18, 2020

0.0.10

Dec 4, 2019

0.0.9

Oct 11, 2019

0.0.8

Sep 4, 2019

0.0.7

Mar 21, 2019

0.0.6

Mar 13, 2019

This version

0.0.5

Mar 11, 2019

0.0.4

Mar 4, 2019

0.0.3

Jan 30, 2019

0.0.2

Oct 20, 2018

0.0.1

Aug 18, 2018

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