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https://github.com/biosimulators/biosimulators_tellurium

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

https://github.com/biosimulators/biosimulators_tellurium

Science Score: 13.0%

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    Scientific vocabulary similarity
    Low similarity (15.6%) to scientific vocabulary

Keywords

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

Keywords from Contributors

logical-model mathematical-model cobrapy constraint-based-modeling fba flux-balance-analysis combine omex copasi gillespy2
Last synced: 5 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 2
  • Watchers: 7
  • Forks: 2
  • Open Issues: 4
  • Releases: 42
Topics
biochemical-networks biosimulators combine-archive computational-biology docker dynamical-modeling libroadrunner omex-metadata python sbml sed-ml simulation systems-biology tellurium
Created almost 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Contributing License Code of conduct

README.md

Latest release PyPI CI status Test coverage All Contributors

BioSimulators-tellurium

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

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

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

Installation

Dependencies

  • Python
  • pip
  • libncurses
  • libxml

Install Python package

pip install biosimulators-tellurium

Install Docker image

docker pull ghcr.io/biosimulators/tellurium

Usage

Local usage

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

BioSimulators-compliant command-line interface to the tellurium simulation program http://tellurium.analogmachine.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/tellurium:latest \ -i /root/in/modeling-study.omex \ -o /root/out

Documentation

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

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 in New York 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
  • Watch event: 1
  • Pull request event: 2
  • Create event: 2
Last Year
  • Watch event: 1
  • Pull request event: 2
  • Create event: 2

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 184
  • Total Committers: 5
  • Avg Commits per committer: 36.8
  • Development Distribution Score (DDS): 0.179
Top Committers
Name Email Commits
Jonathan Karr j****r@g****m 151
biosimulatorsdaemon b****n@g****m 26
Bilal Shaikh b****2@g****m 4
allcontributors[bot] 4****]@u****m 2
0u812 0****2@u****m 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 7
  • Total pull requests: 17
  • Average time to close issues: 4 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 3
  • Total pull request authors: 5
  • Average comments per issue: 2.43
  • Average comments per pull request: 0.65
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 4
Past Year
  • Issues: 0
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: about 3 hours
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.25
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 3
View more stats
Top Authors
Issue Authors
  • jonrkarr (5)
  • gmarupilla (1)
  • luciansmith (1)
Pull Request Authors
  • luciansmith (13)
  • dependabot[bot] (4)
  • 0u812 (1)
  • allcontributors[bot] (1)
  • jonrkarr (1)
Top Labels
Issue Labels
question (2) enhancement (1)
Pull Request Labels
dependencies (4)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 248 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 40
  • Total maintainers: 2
pypi.org: biosimulators-tellurium

BioSimulators-compliant command-line interface to the Tellurium/roadrunner simulator <https://tellurium.readthedocs.io/>.

  • Versions: 40
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 248 Last month
Rankings
Dependent repos count: 9.0%
Dependent packages count: 10.0%
Average: 18.4%
Forks count: 19.1%
Downloads: 22.1%
Stargazers count: 31.9%
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 >=0.1.137
  • kisao >=2.28
  • libroadrunner >=2.1.2
  • lxml *
  • numpy *
  • pandas *
  • rrplugins *
  • tellurium >=2.2.1
tests/requirements.txt pypi
  • biosimulators_utils * test
  • numpy * test
  • pypdf2 * test
  • pyyaml * test
.github/workflows/ci.yml actions
  • actions/cache v3 composite
  • actions/create-release v1 composite
  • actions/setup-python v3 composite
  • ad-m/github-push-action master composite
  • codecov/codecov-action v3 composite
Dockerfile docker
  • python 3.9-slim-buster build
requirements.optional.txt pypi
setup.py pypi