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https://github.com/biosimulators/biosimulators_bionetgen

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

https://github.com/biosimulators/biosimulators_bionetgen

Science Score: 10.0%

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    Low similarity (16.2%) to scientific vocabulary

Keywords

biochemical-networks bionetgen biosimulators combine-archive docker dynamical-modeling network-free-simulation omex-metadata rule-based-modeling sed-ml simulation stochastic-simulation-algorithm systems-biology

Keywords from Contributors

mathematical-model cobrapy computational-biology constraint-based-modeling fba flux-balance-analysis sbml combine omex copasi
Last synced: 5 months ago · JSON representation

Repository

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

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  • Stars: 1
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  • Forks: 2
  • Open Issues: 3
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Fork of ASinanSaglam/BNG_BioSimDocker
Topics
biochemical-networks bionetgen biosimulators combine-archive docker dynamical-modeling network-free-simulation omex-metadata rule-based-modeling sed-ml simulation stochastic-simulation-algorithm systems-biology
Created almost 6 years ago · Last pushed almost 4 years ago
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README.md

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BioSimulators-BioNetGen

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

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

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

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

Installation

Install Python package

After installing BioNetGen, use pip to install this package as illustrated below. pip install biosimulators-bionetgen

Install Docker image

docker pull ghcr.io/biosimulators/bionetgen

Usage

Local usage

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

BioSimulators-compliant command-line interface to the BioNetGen simulation program https://bionetgen.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/bionetgen:latest \ -i /root/in/modeling-study.omex \ -o /root/out

Documentation

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

License

This package is released under the MIT license.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai, Ali Sinan Saglam in the Faeder Lab at the University of Pittsburgh, and the Center for Reproducible Biomedical Modeling with assistance from the contributors listed here.

Questions and comments

Please contact the BioSimulators Team with any questions or comments about the command-line program or Docker image. Please contact Ali Sinan Saglam with any questions or comments about BioNetGen.

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

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Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 160
  • Total Committers: 4
  • Avg Commits per committer: 40.0
  • Development Distribution Score (DDS): 0.219
Top Committers
Name Email Commits
Jonathan Karr j****r@g****m 125
biosimulatorsdaemon b****n@g****m 21
Ali Sinan Saglam a****m@g****m 8
Bilal Shaikh b****2@g****m 6

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 5
  • Total pull requests: 0
  • Average time to close issues: about 1 hour
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.4
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • jonrkarr (4)
  • TorkelE (1)
Pull Request Authors
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Issue Labels
enhancement (1)
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 327 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 21
  • Total maintainers: 2
pypi.org: biosimulators-bionetgen

BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.

  • Versions: 21
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 327 Last month
Rankings
Dependent repos count: 9.0%
Dependent packages count: 10.1%
Average: 18.2%
Forks count: 19.1%
Downloads: 21.1%
Stargazers count: 31.9%
Maintainers (2)
biosimulators jonrkarr
Last synced: 7 months ago