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colomoto-docker

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

https://github.com/colomoto/colomoto-docker

Science Score: 59.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 11 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 8 committers (12.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary

Keywords

biological-networks docker jupyter-notebook model-analysis systems-biology

Keywords from Contributors

standardization interpretability meshing finite-volume animal office data-profilers hack autograder report
Last synced: 6 months ago · JSON representation

Repository

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Basic Info
Statistics
  • Stars: 27
  • Watchers: 6
  • Forks: 13
  • Open Issues: 4
  • Releases: 48
Topics
biological-networks docker jupyter-notebook model-analysis systems-biology
Created over 8 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing

README.md

The CoLoMoTo Docker and Notebook

PyPI version Binder DOI:10.3389/fphys.2018.00680 DOI:10.5281/zenodo.17035228

The CoLoMoTo Interactive Notebook relies on Docker and Jupyter technologies to provide a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks.

Quick usage guide

You need Docker and Python. We support GNU/Linux, macOS, and Windows.

Install the helper script in a terminal:

pip install -U colomoto-docker    # or python3 -m pip install ..

The CoLoMoTo notebook can be started by executing in a terminal (if using Docker Toolbox, in a Docker Terminal):

colomoto-docker

The container can be stopped by pressing Ctrl+C keys.

A specific tag can be specified using the -V option. For example:

colomoto-docker -V latest       # fetches the latest published image
colomoto-docker -V 2024-04-01   # fetches a specific image
colomto-docker --doi 10.5281/zenodo.17035229   # fetches image from Zenodo record

Warning: by default, the files within the Docker container are isolated from the running host computer, therefore files are deleted after stopping the container, except the files within the persistent directory.

To have access to the files of your current directory you can use the --bind option:

colomoto-docker --bind .

See usage guide for further options and alternative methods.

Docker images are persistently archived on Zenodo at https://doi.org/10.5281/zenodo.17035228.

Contribute

See how to add your tool.

Owner

  • Name: Consortium for Logical Models and Tools
  • Login: colomoto
  • Kind: organization

GitHub Events

Total
  • Create event: 11
  • Issues event: 2
  • Release event: 5
  • Watch event: 1
  • Delete event: 8
  • Issue comment event: 9
  • Push event: 73
  • Pull request event: 13
  • Fork event: 1
Last Year
  • Create event: 11
  • Issues event: 2
  • Release event: 5
  • Watch event: 1
  • Delete event: 8
  • Issue comment event: 9
  • Push event: 73
  • Pull request event: 13
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 552
  • Total Committers: 8
  • Avg Commits per committer: 69.0
  • Development Distribution Score (DDS): 0.295
Past Year
  • Commits: 46
  • Committers: 4
  • Avg Commits per committer: 11.5
  • Development Distribution Score (DDS): 0.587
Top Committers
Name Email Commits
Loïc Paulevé l****e@e****g 389
Loïc Paulevé l****e@l****r 69
Aurelien Naldi a****i@g****m 41
github-actions[bot] 4****] 29
Celine Hernandez c****z@e****r 15
Samuel Pastva s****a@g****m 6
GitHub Action a****n@g****m 2
pauleve p****e 1
Committer Domains (Top 20 + Academic)
github.com: 1 ens.fr: 1 labri.fr: 1 ens-cachan.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 40
  • Total pull requests: 104
  • Average time to close issues: 11 months
  • Average time to close pull requests: 20 days
  • Total issue authors: 7
  • Total pull request authors: 6
  • Average comments per issue: 2.78
  • Average comments per pull request: 0.39
  • Merged pull requests: 80
  • Bot issues: 1
  • Bot pull requests: 47
Past Year
  • Issues: 2
  • Pull requests: 13
  • Average time to close issues: 5 days
  • Average time to close pull requests: 12 days
  • Issue authors: 2
  • Pull request authors: 4
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.46
  • Merged pull requests: 8
  • Bot issues: 1
  • Bot pull requests: 6
View more stats
Top Authors
Issue Authors
  • pauleve (29)
  • aurelien-naldi (3)
  • xhajnal (3)
  • chernan (2)
  • jonrkarr (1)
  • github-actions[bot] (1)
  • lunaticstarr (1)
Pull Request Authors
  • github-actions[bot] (47)
  • pauleve (45)
  • daemontus (5)
  • aurelien-naldi (5)
  • szlaura (1)
  • bblodfon (1)
Top Labels
Issue Labels
architecture (11) tool request (6) pkg-update (4) enhancement (4) bug (3) low-priority (2) tool (2) QA (2) help wanted (2)
Pull Request Labels
ready-for-monthly-merge (32) pkg-update (30) auto (24) tool (7) architecture (3) tool request (1) low-priority (1) QA (1) invalid (1)

Dependencies

.github/workflows/auto-tag.yml actions
  • actions-hub/docker master composite
  • actions-hub/docker/login master composite
  • actions/checkout v2 composite
.github/workflows/auto-update.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • peter-evans/create-pull-request v3.5.0 composite
.github/workflows/dockerimage-next.yml actions
  • actions-hub/docker master composite
  • actions-hub/docker/login master composite
  • actions/checkout v1 composite
.github/workflows/for-next.yml actions
  • actions/checkout v2 composite
.github/workflows/mirror-ghcr.yml actions
  • actions-hub/docker master composite
  • actions-hub/docker/login master composite
.github/workflows/monthly-merge.yml actions
  • pascalgn/automerge-action v0.13.0 composite
.github/workflows/release.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • softprops/action-gh-release v1 composite
.github/workflows/validate-pr.yml actions
  • actions-hub/docker master composite
  • actions-hub/docker/login master composite
  • actions/checkout v1 composite
Dockerfile docker
  • debian stable-20220328-slim build
setup.py pypi