pypesto

python Parameter EStimation TOolbox

https://github.com/icb-dcm/pypesto

Science Score: 85.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 19 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
6 of 31 committers (19.4%) from academic institutions
✓
Institutional organization owner
Organization icb-dcm has institutional domain (www.mathematics-and-life-sciences.uni-bonn.de)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary

Keywords

hacktoberfest optimization parameter-estimation python systems-biology

Keywords from Contributors

cvode ode sbml petab differentialequations sensitivity-analysis systemsbiology sensitivities pysb mechanistic-models

Last synced: 4 months ago · JSON representation ·

Repository

python Parameter EStimation TOolbox

Basic Info

Host: GitHub
Owner: ICB-DCM
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://pypesto.readthedocs.io
Size: 45.5 MB

Statistics

Stars: 256
Watchers: 13
Forks: 47
Open Issues: 142
Releases: 45

Topics

hacktoberfest optimization parameter-estimation python systems-biology

Created over 7 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog License Citation Codeowners

pyPESTO - Parameter EStimation TOolbox for python

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

Feature overview

Feature overview of pyPESTO. Figure taken from the Bioinformatics publication.

pyPESTO features include:

Parameter estimation interfacing multiple optimization algorithms including multi-start local and global optimization. (example, overview of optimizers)
Interface to multiple simulators including
- AMICI for efficient simulation and sensitivity analysis of ordinary differential equation (ODE) models. (example)
- RoadRunner for simulation of SBML models. (example)
- Jax and Julia for automatic differentiation.
Uncertainty quantification using various methods:
- Profile likelihoods.
- Sampling using Markov chain Monte Carlo (MCMC), parallel tempering, and interfacing other samplers including emcee, pymc and dynesty. (example)
- Variational inference
Complete parameter estimation pipeline for systems biology problems specified in SBML and PEtab. (example)
Parameter estimation pipelines for different modes of data:
- Relative (scaled and offset) data as described in Schmiester et al. (2020). (example)
- Ordinal data as described in Schmiester et al. (2020) and Schmiester et al. (2021). (example)
- Censored data. (example)
- Semiquantitative data as described in Doresic et al. (2024). (example)
Model selection. (example)
Various visualization methods to analyze parameter estimation results.

Quick install

The simplest way to install pyPESTO is via pip:

shell 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

How to Cite

Citeable DOI for the latest pyPESTO release:

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.

References

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

Owner

Name: Data-driven Computational Modelling
Login: ICB-DCM
Kind: organization

Website: https://www.mathematics-and-life-sciences.uni-bonn.de/de?setlanguage=en
Repositories: 13
Profile: https://github.com/ICB-DCM

Hasenauer Lab @ University of Bonn / Helmholtz Munich

Citation (CITATION.cff)

message: If you use this software, please cite it using these metadata.
authors:
   -
      family-names: "Schälte"
      given-names: "Yannik"
      orcid: "https://orcid.org/0000-0003-1293-820X"
   -
      family-names: "Fröhlich"
      given-names: "Fabian"
      orcid: "https://orcid.org/0000-0002-5360-4292"
   -
      family-names: "Stapor"
      given-names: "Paul"
      orcid: "https://orcid.org/0000-0002-7567-3985"
   -
      family-names: "Vanhoefer"
      given-names: "Jakob"
      orcid: "https://orcid.org/0000-0002-3451-1701"
   -
      family-names: "Weindl"
      given-names: "Daniel"
      orcid: "https://orcid.org/0000-0001-9963-6057"
   -
      family-names: "Jost"
      given-names: "Paul Jonas"
      orcid: "https://orcid.org/0000-0001-7613-6244"
   -
      family-names: "Wang"
      given-names: "Dantong"
      orcid: "https://orcid.org/0000-0002-3277-5033"
   -
      family-names: "Lakrisenko"
      given-names: "Polina"
      orcid: "https://orcid.org/0000-0002-7626-8420"
   -
      family-names: "Raimúndez"
      given-names: "Elba"
      orcid: "https://orcid.org/0000-0002-2790-6668"
   -
      family-names: "Pathirana"
      given-names: "Dilan"
      orcid: "https://orcid.org/0000-0001-7000-2659"
   -
      family-names: "Schmiester"
      given-names: "Leonard"
      orcid: "https://orcid.org/0000-0001-7946-3232"
   -
      family-names: "Städter"
      given-names: "Philipp"
      orcid: "https://orcid.org/0000-0002-4586-6604"
   -
      family-names: "Contento"
      given-names: "Lorenzo"
      orcid: "https://orcid.org/0000-0002-7901-2172"
   -
      family-names: "Merkt"
      given-names: "Simon"
      orcid: "https://orcid.org/0000-0002-8017-4494"
   -
      family-names: "Dudkin"
      given-names: "Erika"
      orcid: "https://orcid.org/0000-0002-9649-0029"
   -
      family-names: "Grein"
      given-names: "Stephan"
      orcid: "https://orcid.org/0000-0001-9524-6633"
   -
      family-names: "Hasenauer"
      given-names: "Jan"
      orcid: "https://orcid.org/0000-0002-4935-3312"
title: "pyPESTO - Parameter EStimation TOolbox for python"
url: "https://github.com/ICB-DCM/pyPESTO"
doi: 10.5281/zenodo.2553546
cff-version: 1.2.0

GitHub Events

Total

Create event: 79
Release event: 3
Issues event: 47
Watch event: 33
Delete event: 82
Member event: 2
Issue comment event: 130
Push event: 214
Pull request event: 133
Pull request review event: 175
Pull request review comment event: 120
Fork event: 1

Last Year

Create event: 79
Release event: 3
Issues event: 47
Watch event: 33
Delete event: 82
Member event: 2
Issue comment event: 130
Push event: 214
Pull request event: 133
Pull request review event: 175
Pull request review comment event: 120
Fork event: 1

Committers

Last synced: 7 months ago

All Time

Total Commits: 1,262
Total Committers: 31
Avg Commits per committer: 40.71
Development Distribution Score (DDS): 0.651

Past Year

Commits: 108
Committers: 10
Avg Commits per committer: 10.8
Development Distribution Score (DDS): 0.546

Top Committers

Name	Email	Commits
yannikschaelte	y**e@g**m	440
Daniel Weindl	d****l	231
Paul Jonas Jost	7****t	177
Fabian Fröhlich	f**n@s**m	85
Dilan Pathirana	5****h	56
Paul Stapor	p**r@h**e	46
Jakob Vanhoefer	3****r	42
Doresic	8****c	31
Polina Lakrisenko	p**o@g**m	25
Fabian Fröhlich	f**h@h**u	24
Dantong Wang	d**g@h**e	17
Elba Raimúndez Alvarez	e**z@h**e	11
Jonas Arruda	6****n	11
Maren Philipps	5****s	10
dependabot[bot]	4****]	9
Stephan Grein	s**n@u**e	9
Simon Merkt	4****n	6
LeonardSchmiester	l**r@h**e	5
Vincent Wieland	v**7@w**e	5
Lorenzo Contento	l****o	3
PhilippStaedter	4****r	3
Wang	d**g@s**e	3
C-Peiter	8****r	2
DantongWang	3****g	2
Sebastian Höpfl	6****l	2
Theorell	a**l@g**m	2
ErikaDudkin	4****i	1
Giacomo Fabrini	6****i	1
Kristian Meyer	8****t	1
Lea Seep	7****p	1
and 1 more...

Committer Domains (Top 20 + Academic)

helmholtz-muenchen.de: 4 scidom.de: 1 uni-bonn.de: 1 hms.harvard.edu: 1 schaluck.com: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 190
Total pull requests: 407
Average time to close issues: 6 months
Average time to close pull requests: about 1 month
Total issue authors: 38
Total pull request authors: 22
Average comments per issue: 2.21
Average comments per pull request: 1.53
Merged pull requests: 348
Bot issues: 0
Bot pull requests: 10

Past Year

Issues: 43
Pull requests: 129
Average time to close issues: about 1 month
Average time to close pull requests: 15 days
Issue authors: 11
Pull request authors: 11
Average comments per issue: 0.93
Average comments per pull request: 1.31
Merged pull requests: 106
Bot issues: 0
Bot pull requests: 4

View more stats

Top Authors

Issue Authors

dweindl (93)
PaulJonasJost (14)
yannikschaelte (13)
dilpath (9)
FFroehlich (8)
arrjon (7)
shoepfl (7)
paulstapor (6)
Mjvolk3 (5)
m-philipps (5)
jvanhoefer (4)
vwiela (4)
plakrisenko (3)
aidinbii (3)
Doresic (2)

Pull Request Authors

dweindl (217)
PaulJonasJost (168)
Doresic (35)
dilpath (29)
dependabot[bot] (18)
arrjon (17)
plakrisenko (16)
m-philipps (15)
stephanmg (10)
yannikschaelte (9)
FFroehlich (5)
vwiela (4)
shoepfl (3)
MerktSimon (3)
jvanhoefer (3)

Top Labels

Issue Labels

fixed but not released (51) enhancement (50) bug (33) CI (23) question (20) optimization (20) documentation (18) profiling (11) visualization (11) sampling (11) PEtab (10) hierarchical (7) AMICI (5) ensembles (5) good first issue (3) help wanted (3) performance (2) wontfix (1) Julia (1)

Pull Request Labels

dependencies (18) bug (8) enhancement (7) invalid (4) sampling (3) visualization (2) CI (2) Citation (2) AMICI (1) documentation (1)

Packages

Total packages: 1
Total downloads:
- pypi 486 last-month

Total dependent packages: 2
Total dependent repositories: 3
Total versions: 46
Total maintainers: 3

pypi.org: pypesto

python-based Parameter EStimation TOolbox

Homepage: https://github.com/icb-dcm/pypesto
Documentation: https://pypesto.readthedocs.io
License: BSD-3-Clause
Latest release: 0.5.6
published 7 months ago

Versions: 46
Dependent Packages: 2
Dependent Repositories: 3
Downloads: 486 Last month

Rankings

Dependent packages count: 3.2%

Stargazers count: 5.3%

Forks count: 6.3%

Average: 7.3%

Dependent repos count: 9.1%

Downloads: 12.4%

Maintainers (3)

dweindl ffroehlich PaulJonasJost

Last synced: 4 months ago

pypesto

Science Score: 85.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

pyPESTO - Parameter EStimation TOolbox for python

Feature overview

Quick install

Documentation

Examples

Contributing

How to Cite

References

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: pypesto

Rankings

Maintainers (3)