pyABC

pyABC: Efficient and robust easy-to-use approximate Bayesian computation - Published in JOSS (2022)

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

Science Score: 98.0%

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

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
8 of 14 committers (57.1%) from academic institutions
✓
Institutional organization owner
Organization icb-dcm has institutional domain (www.mathematics-and-life-sciences.uni-bonn.de)
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

abc approximate-bayesian-inference likelihood-free-inference parameter-inference

Last synced: 6 months ago · JSON representation

Repository

distributed, likelihood-free inference

Basic Info

Host: GitHub
Owner: ICB-DCM
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://pyabc.rtfd.io
Size: 46.5 MB

Statistics

Stars: 216
Watchers: 5
Forks: 45
Open Issues: 36
Releases: 65

Topics

abc approximate-bayesian-inference likelihood-free-inference parameter-inference

Created over 8 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog License

pyABC

pyABC is a massively parallel, distributed, and scalable ABC-SMC (Approximate Bayesian Computation - Sequential Monte Carlo) framework for parameter estimation of complex stochastic models. It provides numerous state-of-the-art algorithms for efficient, accurate, robust likelihood-free inference, described in the documentation and illustrated in example notebooks. Written in Python, with support for integration with R and Julia.

Resources

📖 Documentation: https://pyabc.rtfd.io
💡 Examples: https://pyabc.rtfd.io/en/latest/examples.html
💬 Contact: https://pyabc.rtfd.io/en/latest/about.html
🐛 Bug Reports: https://github.com/icb-dcm/pyabc/issues
💻 Source Code: https://github.com/icb-dcm/pyabc
📄 Cite: https://pyabc.rtfd.io/en/latest/cite.html

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

JOSS Publication

pyABC: Efficient and robust easy-to-use approximate Bayesian computation

Published

June 25, 2022

DOI

10.21105/joss.04304

Volume 7, Issue 74, Page 4304

Authors

Yannik Schälte

Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany, Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany, Center for Mathematics, Technical University Munich, Garching, Germany

Emmanuel Klinger
Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany, Center for Mathematics, Technical University Munich, Garching, Germany, Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany

Emad Alamoudi

Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany

Jan Hasenauer

Editor

Øystein Sørensen

Papers & Mentions

Total mentions: 1

Rethinking multiscale cardiac electrophysiology with machine learning and predictive modelling

DOI: 10.1016/j.compbiomed.2018.10.015
OpenAlex ID: https://openalex.org/W2896792008
Published: January 2019

Last synced: 4 months ago

GitHub Events

Total

Create event: 5
Release event: 1
Issues event: 6
Watch event: 11
Delete event: 2
Issue comment event: 29
Push event: 66
Pull request review event: 13
Pull request review comment event: 4
Pull request event: 17
Fork event: 1

Last Year

Create event: 5
Release event: 1
Issues event: 6
Watch event: 11
Delete event: 2
Issue comment event: 29
Push event: 66
Pull request review event: 13
Pull request review comment event: 4
Pull request event: 17
Fork event: 1

Committers

Last synced: 7 months ago

All Time

Total Commits: 1,427
Total Committers: 14
Avg Commits per committer: 101.929
Development Distribution Score (DDS): 0.518

Past Year

Commits: 82
Committers: 2
Avg Commits per committer: 41.0
Development Distribution Score (DDS): 0.22

Top Committers

Name	Email	Commits
yannikschaelte	y**e@g**m	688
neuralyzer	e**r@g**m	581
Stephan Grein	s**n@u**e	81
dennis	d**t@h**e	26
arrjon	j**a@u**e	19
yannikschaelte	y**e@h**e	12
Emad Alamoudi	e**4@h**m	11
Daniel Weindl	d****l	2
neuralyzer	e**r@b**e	2
Fabian Rost	f**t@t**e	1
Felipe	6****8	1
Pariksheet Nanda	p**a@u**u	1
Pat Laub	p**b@g**m	1
Elba Raimúndez Alvarez	e**z@h**e	1

Committer Domains (Top 20 + Academic)

helmholtz-muenchen.de: 3 uni-bonn.de: 2 umich.edu: 1 tu-dresden.de: 1 brain.mpg.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 74
Total pull requests: 83
Average time to close issues: 8 months
Average time to close pull requests: about 1 month
Total issue authors: 31
Total pull request authors: 7
Average comments per issue: 3.2
Average comments per pull request: 1.46
Merged pull requests: 76
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 14
Average time to close issues: 8 days
Average time to close pull requests: 5 days
Issue authors: 3
Pull request authors: 3
Average comments per issue: 1.33
Average comments per pull request: 2.36
Merged pull requests: 12
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

yannikschaelte (25)
xieduo7 (7)
Gabriel-p (6)
omsai (4)
EmadAlamoudi (3)
samufi (2)
stephanmg (2)
jack-pan-ai (2)
ljschumacher (2)
blakeaw (2)
HounerX (2)
vesmanojlovic (1)
lm1909 (1)
MG-dkfz (1)
anetzl (1)

Pull Request Authors

yannikschaelte (52)
stephanmg (19)
EmadAlamoudi (8)
arrjon (3)
PaulJonasJost (2)
dweindl (2)
omsai (1)
lcontento (1)

Top Labels

Issue Labels

enhancement (26) bug (19) documentation (4) wontfix (3) visualization (3) question (2) fixed but not released (1)

Pull Request Labels

bug (2) enhancement (2) documentation (1)

Packages

Total packages: 1
Total downloads:
- pypi 3,984 last-month

Total dependent packages: 3
Total dependent repositories: 9
Total versions: 113
Total maintainers: 5

pypi.org: pyabc

Distributed, likelihood-free ABC-SMC inference

Homepage: https://github.com/icb-dcm/pyabc
Documentation: https://pyabc.readthedocs.io
License: BSD-3-Clause
Latest release: 0.12.16
published 9 months ago

Versions: 113
Dependent Packages: 3
Dependent Repositories: 9
Downloads: 3,984 Last month

Rankings

Dependent packages count: 2.4%

Dependent repos count: 4.9%

Stargazers count: 5.1%

Average: 5.3%

Forks count: 6.3%

Downloads: 7.6%

Maintainers (5)

elbaraim neuralyzer yannik.schaelte stephanmg arrjon

Last synced: 6 months ago

Dependencies

requirements-dev.txt pypi

pre-commit >=2.10.1 development
tox >=3.21.4 development

.github/workflows/ci.yml actions

actions/cache v1 composite
actions/checkout v2 composite
actions/setup-python v1 composite
codecov/codecov-action v2 composite
julia-actions/setup-julia v1 composite

.github/workflows/deploy.yml actions

actions/checkout v2 composite
actions/setup-python v1 composite

pyABC

Science Score: 98.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

pyABC

Resources

Owner

JOSS Publication

pyABC: Efficient and robust easy-to-use approximate Bayesian computation

Authors

Editor

Tags

Papers & Mentions

Rethinking multiscale cardiac electrophysiology with machine learning and predictive modelling

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: pyabc

Rankings

Maintainers (5)

Dependencies