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https://github.com/biosimulators/biosimulators_cobrapy

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

https://github.com/biosimulators/biosimulators_cobrapy

Science Score: 10.0%

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Keywords

biochemical-networks biosimulators cobrapy combine-archive computational-biology constraint-based-modeling docker fba flux-balance-analysis omex-metadata python sbml sed-ml simulation systems-biology
Last synced: 5 months ago · JSON representation

Repository

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

Basic Info
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  • Stars: 2
  • Watchers: 5
  • Forks: 0
  • Open Issues: 2
  • Releases: 0
Topics
biochemical-networks biosimulators cobrapy combine-archive computational-biology constraint-based-modeling docker fba flux-balance-analysis omex-metadata python sbml sed-ml simulation systems-biology
Created almost 6 years ago · Last pushed almost 4 years ago
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README.md

Latest release PyPI CI status Test coverage All Contributors

BioSimulators-COBRApy

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

This command-line interface and Docker image enable users to use COBRApy 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 COBRApy is available at BioSimulators.

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

Installation

Install Python package

pip install biosimulators-cobrapy

Install Docker image

docker pull ghcr.io/biosimulators/cobrapy

Usage

SED-ML targets for simulation predictions

BioSimulators-COBRApy recognizes the following targets for simulation predictions:

  • FBA (KISAO_0000437), parsimonious FBA (KISAO_0000528), geometric FBA (KISAO_0000527):
    • Objective: fbc:objective/@value
    • Reaction flux: sbml:reaction/@flux
    • Reaction reduced cost: sbml:reaction/@reducedCost
    • Species shadow price: sbml:species/@shadowPrice
  • FVA (KISAO_0000526):
    • Minimum reaction flux: sbml:reaction/@minFlux
    • Maximum reaction flux: sbml:reaction/@maxFlux

Please see https://docs.biosimulations.org for more information.

Local usage

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

BioSimulators-compliant command-line interface to the COBRApy simulation program https://opencobra.github.io/cobrapy/.

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/cobrapy:latest \ -i /root/in/modeling-study.omex \ -o /root/out

Documentation

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

License

This package is released under the MIT license.

Development team

This package was developed by the Center for Reproducible Biomedical Modeling and the Karr Lab at the Icahn School of Medicine at Mount Sinai 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

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Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 197
  • Total Committers: 5
  • Avg Commits per committer: 39.4
  • Development Distribution Score (DDS): 0.305
Top Committers
Name Email Commits
Jonathan Karr j****r@g****m 137
AzrafAnwar a****1@c****u 30
biosimulatorsdaemon b****n@g****m 26
Bilal Shaikh b****2@g****m 3
Moritz E. Beber m****r@p****t 1
Committer Domains (Top 20 + Academic)
posteo.net: 1 columbia.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 3
  • Total pull requests: 2
  • Average time to close issues: 2 months
  • Average time to close pull requests: 28 minutes
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • 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
View more stats
Top Authors
Issue Authors
  • jonrkarr (3)
Pull Request Authors
  • Midnighter (1)
  • jonrkarr (1)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 421 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 24
  • Total maintainers: 2
pypi.org: biosimulators-cobrapy

BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.

  • Versions: 24
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 421 Last month
Rankings
Dependent repos count: 9.0%
Dependent packages count: 10.1%
Downloads: 18.5%
Average: 19.0%
Stargazers count: 27.8%
Forks count: 29.8%
Maintainers (2)
biosimulators jonrkarr
Last synced: 6 months ago

Dependencies

docs-src/requirements.txt pypi
  • pydata-sphinx-theme *
  • sphinx >=1.8
  • sphinxprettysearchresults *
requirements.optional.txt pypi
  • gurobipy *
requirements.txt pypi
  • biosimulators_utils >=0.1.162
  • cobra *
  • kisao *
  • lxml *
  • numpy *
  • python_libsbml *
tests/requirements.txt pypi
  • attrdict * test
  • biosimulators_utils * test
  • python_dateutil * test