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https://github.com/biosimulators/biosimulators_copasi

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

https://github.com/biosimulators/biosimulators_copasi

Science Score: 36.0%

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    CITATION.cff file
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    Found .zenodo.json file
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    Committers with academic emails
    2 of 10 committers (20.0%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (15.6%) to scientific vocabulary

Keywords

biochemical-networks biosimulators combine-archive computational-biology copasi docker dynamical-modeling omex-metadata python sbml sed-ml simulation systems-biology

Keywords from Contributors

mathematical-models cobrapy constraint-based-modeling fba flux-balance-analysis combine omex
Last synced: 5 months ago · JSON representation

Repository

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Basic Info
Statistics
  • Stars: 2
  • Watchers: 5
  • Forks: 3
  • Open Issues: 8
  • Releases: 36
Topics
biochemical-networks biosimulators combine-archive computational-biology copasi docker dynamical-modeling omex-metadata python sbml sed-ml simulation systems-biology
Created about 6 years ago · Last pushed 8 months ago
Metadata Files
Readme Contributing License Code of conduct

README.md

Latest release PyPI CI status Test coverage All Contributors

BioSimulators-COPASI

BioSimulators-compliant command-line interface and Docker image for the COPASI simulation program.

This command-line interface and Docker image enable users to use COPASI to execute COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more models (in SBML format).

A list of the algorithms and algorithm parameters supported by COPASI is available at BioSimulators.

A simple web application and web service for using COPASI to execute COMBINE/OMEX archives is also available at runBioSimulations.

Installation

Install Python package

pip install biosimulators-copasi

Install Docker image

docker pull ghcr.io/biosimulators/copasi

Usage

Local usage

``` usage: biosimulators-copasi [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the COPASI simulation program http://copasi.org.

optional arguments: -h, --help show this help message and exit -d, --debug full application debug mode -q, --quiet suppress all console output -i ARCHIVE, --archive ARCHIVE Path to OMEX file which contains one or more SED-ML- encoded simulation experiments -o OUTDIR, --out-dir OUTDIR Directory to save outputs -v, --version show program's version number and exit ```

Usage through Docker container

The entrypoint to the Docker image supports the same command-line interface described above.

For example, the following command could be used to use the Docker image to execute the COMBINE/OMEX archive ./modeling-study.omex and save its outputs to ./.

docker run \ --tty \ --rm \ --mount type=bind,source="$(pwd)",target=/root/in,readonly \ --mount type=bind,source="$(pwd)",target=/root/out \ ghcr.io/biosimulators/copasi:latest \ -i /root/in/modeling-study.omex \ -o /root/out

Documentation

Documentation is available at https://docs.biosimulators.org/Biosimulators_COPASI/.

License

This package is released under the MIT license. COPASI is released under the Artistic 2.0 License.

Development team

This package was developed by the Center for Reproducible Biomedical Modeling. COPASI was developed by a team at the University of Connecticut, the University of Heidelberg, and the University of Virginia with assistance from the contributors listed here.

Questions and comments

Please contact the BioSimulators Team with any questions or comments.

Owner

  • Name: BioSimulators
  • Login: biosimulators
  • Kind: organization
  • Email: info@biosimulators.org
  • Location: USA

Enabling more comprehensive and more predictive biological models through standardized simulation tools

GitHub Events

Total
  • Delete event: 2
  • Issue comment event: 6
  • Push event: 7
  • Pull request review event: 1
  • Pull request event: 7
  • Create event: 5
Last Year
  • Delete event: 2
  • Issue comment event: 6
  • Push event: 7
  • Pull request review event: 1
  • Pull request event: 7
  • Create event: 5

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 394
  • Total Committers: 10
  • Avg Commits per committer: 39.4
  • Development Distribution Score (DDS): 0.467
Top Committers
Name Email Commits
Jonathan Karr j****r@g****m 210
gmarupilla m****a@u****u 107
biosimulatorsdaemon b****n@g****m 37
GMarupilla 5****a@u****m 18
GMarupilla m****a@m****m 10
Frank T. Bergmann f****n@c****u 6
github-actions[bot] 4****]@u****m 3
Bilal Shaikh b****2@g****m 1
Mike Wilson m****6@u****m 1
Jürgen Pahle g****t@p****e 1
Committer Domains (Top 20 + Academic)
pahle.de: 1 caltech.edu: 1 mail.com: 1 uchc.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 38
  • Total pull requests: 43
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 22 days
  • Total issue authors: 8
  • Total pull request authors: 10
  • Average comments per issue: 2.5
  • Average comments per pull request: 1.35
  • Merged pull requests: 34
  • Bot issues: 5
  • Bot pull requests: 11
Past Year
  • Issues: 0
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 month
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 1.5
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 5
View more stats
Top Authors
Issue Authors
  • jonrkarr (16)
  • gmarupilla (8)
  • todo[bot] (5)
  • AlexPatrie (3)
  • fbergmann (2)
  • luciansmith (2)
  • eagmon (1)
  • leon9812 (1)
Pull Request Authors
  • AlexPatrie (12)
  • gmarupilla (11)
  • dependabot[bot] (8)
  • github-actions[bot] (6)
  • CodeByDrescher (3)
  • fbergmann (3)
  • luciansmith (2)
  • jonrkarr (1)
  • bilalshaikh42 (1)
  • jpahle (1)
Top Labels
Issue Labels
todo :spiral_notepad: (6) enhancement (5) discussion (2) documentation (1)
Pull Request Labels
dependencies (8) python (5) documentation (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 471 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 48
  • Total maintainers: 2
pypi.org: biosimulators-copasi

BioSimulators-compliant command-line interface to the COPASI simulation program <http://copasi.org>.

  • Versions: 48
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 471 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 11.6%
Downloads: 11.6%
Average: 15.6%
Forks count: 16.8%
Stargazers count: 27.8%
Maintainers (2)
biosimulators jonrkarr
Last synced: 6 months ago

Dependencies

docs-src/requirements.txt pypi
  • pydata-sphinx-theme *
  • sphinx >=1.8
  • sphinxprettysearchresults *
requirements.txt pypi
  • biosimulators_utils >=0.1.128
  • kisao *
  • lxml *
  • numpy *
  • python_copasi >=4.33.246
tests/requirements.txt pypi
  • biosimulators_utils * test
  • python_dateutil * test
.github/workflows/ci.yml actions
  • actions/create-release v1 composite
  • actions/setup-python v2 composite
  • ad-m/github-push-action master composite
  • andymckay/cancel-action 0.2 composite
  • codecov/codecov-action v2 composite
Dockerfile docker
  • python 3.9-slim-buster build
requirements.optional.txt pypi
setup.py pypi