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https://github.com/biosimulators/biosimulators_pysces

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

https://github.com/biosimulators/biosimulators_pysces

Science Score: 13.0%

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    Low similarity (16.1%) to scientific vocabulary

Keywords

biochemical-network biosimulators combine computational-biology kinetic-model mathematical-model omex sbml sed-ml simulation systems-biology
Last synced: 5 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 2
  • Watchers: 3
  • Forks: 0
  • Open Issues: 2
  • Releases: 32
Topics
biochemical-network biosimulators combine computational-biology kinetic-model mathematical-model omex sbml sed-ml simulation systems-biology
Created over 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License Code of conduct

README.md

Latest release PyPI CI status Test coverage All Contributors

BioSimulators-PySCeS

BioSimulators-compliant command-line interface to the PySCeS simulation program.

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

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

Installation

Install Python package

pip install biosimulators-pysces

Install Docker image

docker pull ghcr.io/biosimulators/pysces

Usage

Local usage

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

BioSimulators-compliant command-line interface to the PySCeS simulation program http://pysces.sourceforge.net/.

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

Documentation

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

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
  • Create event: 2
  • Issues event: 1
  • Release event: 2
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 6
  • Push event: 14
  • Pull request event: 4
Last Year
  • Create event: 2
  • Issues event: 1
  • Release event: 2
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 6
  • Push event: 14
  • Pull request event: 4

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 161
  • Total Committers: 2
  • Avg Commits per committer: 80.5
  • Development Distribution Score (DDS): 0.193
Top Committers
Name Email Commits
Jonathan Karr j****r@g****m 130
biosimulatorsdaemon b****n@g****m 31

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 6
  • Total pull requests: 3
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 3 minutes
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 8.0
  • Average comments per pull request: 0.67
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jonrkarr (4)
  • luciansmith (2)
Pull Request Authors
  • luciansmith (4)
  • jonrkarr (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 479 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 31
  • Total maintainers: 2
pypi.org: biosimulators-pysces

BioSimulators-compliant command-line interface to the PySCeS simulation program <http://pysces.sourceforge.net/>.

  • Versions: 31
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 479 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 11.5%
Downloads: 20.2%
Average: 20.7%
Forks count: 29.8%
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 >=0.1.128
  • kisao *
  • lxml *
  • numpy *
  • pysces >=1.0.0
tests/requirements.txt pypi
  • biosimulators_utils * test
  • numpy * test
  • python_dateutil * test
.github/workflows/ci.yml actions
  • actions/cache v2 composite
  • actions/create-release v1 composite
  • actions/setup-python v3 composite
  • ad-m/github-push-action master composite
  • codecov/codecov-action v2 composite
  • emilioschepis/wait-for-endpoint v1.0.3 composite
  • nick-invision/retry v2 composite
  • whoan/docker-build-with-cache-action v5 composite
Dockerfile docker
  • ghcr.io/biosimulators/biosimulators_pysces/pysces_base latest build
requirements.optional.txt pypi
setup.py pypi