JOSS: https://github.com/biocircuits/bioscrape/

chemical-reaction-networks crn cython parameter-identification python simulation stochastic-simulation-algorithm

Score: 6.340359303727752

Last synced: about 8 hours ago
JSON representation

Repository metadata:

Bioscrape: Biological Modeling, Simulation, and Parameter Estimation

Host: GitHub
URL: https://github.com/biocircuits/bioscrape/
Owner: biocircuits
License: mit
Created: 2018-05-04T21:43:17.000Z (over 8 years ago)
Default Branch: main
Last Pushed: 2026-08-20T05:02:46.000Z (2 days ago)
Last Synced: 2026-08-21T07:13:23.841Z (1 day ago)
Topics: chemical-reaction-networks, crn, cython, parameter-identification, python, simulation, stochastic-simulation-algorithm
Language: Jupyter Notebook
Homepage: https://bioscrape.readthedocs.io/en/latest/
Size: 200 MB
Stars: 30
Watchers: 3
Forks: 19
Open Issues: 33
Metadata Files:
- Readme: README.md
- Contributing: contributing.md
- License: LICENSE
- Claude: CLAUDE.md

Owner metadata:

Name: biocircuits
Login: biocircuits
Email:
Kind: organization
Description:
Website:
Location:
Twitter:
Company:
Icon url: https://avatars.githubusercontent.com/u/34864391?v=4
Repositories: 3
Last Synced at: 2023-03-08T23:42:19.450Z
Profile URL: https://github.com/biocircuits

GitHub Events

Total

Create event: 5
Delete event: 3
Fork event: 1
Issue comment event: 14
Issues event: 1
Pull request event: 12
Pull request review event: 6
Push event: 19
Watch event: 11
Total: 72

Last Year

Pull request event: 1
Push event: 1
Watch event: 1
Total: 3

Committers metadata

Last synced: 2 days ago

Total Commits: 429
Total Committers: 9
Avg Commits per committer: 47.667
Development Distribution Score (DDS): 0.473

Commits in past year: 27
Committers in past year: 2
Avg Commits per committer in past year: 13.5
Development Distribution Score (DDS) in past year: 0.37

Name	Email	Commits
ayush9pandey	a**y@g**m	226
sclamons	s**s@g**m	59
William Poole	w**e@c**u	53
William Poole	w**x@h**m	44
Anandh Swaminathan	a**m@g**m	25
Richard Murray	m**y@c**u	18
sclamons	s**s@S**l	2
Ayush Pandey	a**y@g**r	1
Anandh Swaminathan	a**n@A**l	1

Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 64
Total pull requests: 66
Average time to close issues: 8 months
Average time to close pull requests: 14 days
Total issue authors: 13
Total pull request authors: 5
Average comments per issue: 1.81
Average comments per pull request: 1.21
Merged pull request: 56
Bot issues: 0
Bot pull requests: 0

Past year issues: 4
Past year pull requests: 7
Past year average time to close issues: 26 days
Past year average time to close pull requests: about 2 months
Past year issue authors: 1
Past year pull request authors: 2
Past year average comments per issue: 1.25
Past year average comments per pull request: 1.86
Past year merged pull request: 5
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/biocircuits/bioscrape/

Top Issue Authors

ayush9pandey (23)
WilliamIX (14)
sclamons (7)
murrayrm (6)
Robaina (4)
zoltuz (2)
Farnazmdi (2)
sophiejwalton (1)
oliviaywangn (1)
mkratz (1)
SpencerUyematsu (1)
teddiclax (1)
TiamHeydari (1)

Top Pull Request Authors

ayush9pandey (44)
WilliamIX (12)
murrayrm (6)
sclamons (3)
csoneson (1)

Top Issue Labels

Bioscrape Core (16)
enhancement (15)
bug (14)
Lineages (11)
documentation (11)
Analysis Features (5)
Inference (4)
help wanted (3)
question (2)
invalid (1)

Top Pull Request Labels

Bioscrape Core (5)
Analysis Features (5)
enhancement (4)
bug (4)
documentation (3)
Lineages (3)
Inference (2)

Dependencies

requirements.txt pypi

Cython *
beautifulsoup4 *
emcee >=3.0.2
lmfit *
matplotlib *
numpy >=1.16.5
pandas *
pytest *
python-libsbml *
scipy >=1.5.4
sympy *

setup.py pypi

beautifulsoup4 *
cython *
emcee *
matplotlib *
numpy *
pandas *
pytest *
python-libsbml *
scipy *
sympy *

.github/workflows/deploy_bioscrape.yml actions

actions/checkout v3 composite
actions/setup-python v3 composite

.github/workflows/test_bioscrape.yml actions

actions/checkout v3 composite
actions/setup-python v3 composite

pyproject.toml pypi

beautifulsoup4 *
corner *
cython *
emcee *
lmfit *
matplotlib *
numpy *
pandas *
pytest *
python-libsbml *
scipy *
sympy *

.github/workflows/pypi_release.yml actions

actions/checkout v4 composite
pypa/gh-action-pypi-publish release/v1 composite

docs/requirements.txt pypi

ipykernel *
nbconvert *
nbsphinx *
nbsphinx-link *
numpydoc *
recommonmark *
sphinx >=5
sphinx-copybutton *
sphinx-math-dollar *
sphinx-rtd-theme *
sphinx-toggleprompt *

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