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https://github.com/biosimulators/biosimulators_masspy

MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container

https://github.com/biosimulators/biosimulators_masspy

Science Score: 13.0%

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    Low similarity (16.6%) to scientific vocabulary

Keywords

biosimulators combine computational-biology kisao mathematical-model metabolism numerical-simulation omex reaction-network sbml sed-ml systems-biology
Last synced: 5 months ago · JSON representation

Repository

MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 2
  • Releases: 13
Topics
biosimulators combine computational-biology kisao mathematical-model metabolism numerical-simulation omex reaction-network sbml sed-ml systems-biology
Created over 4 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-MASSpy

BioSimulators-compliant command-line interface to the MASSpy simulation program for kinetic simulations of metabolic reaction networks.

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

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

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

Installation

Dependencies

  • Python >= 3.7
  • pip
  • libncurses
  • libxml

Install Python package

pip install biosimulators-masspy

Install Docker image

docker pull ghcr.io/biosimulators/masspy

Usage

Local usage

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

BioSimulators-compliant command-line interface to the MASSpy simulation program https://masspy.readthedocs.io/.

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

Documentation

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

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
  • Release event: 6
  • Delete event: 6
  • Issue comment event: 1
  • Push event: 25
  • Pull request event: 6
  • Create event: 9
Last Year
  • Release event: 6
  • Delete event: 6
  • Issue comment event: 1
  • Push event: 25
  • Pull request event: 6
  • Create event: 9

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 65
  • Total Committers: 2
  • Avg Commits per committer: 32.5
  • Development Distribution Score (DDS): 0.169
Top Committers
Name Email Commits
Jonathan Karr j****r@g****m 54
biosimulatorsdaemon b****n@g****m 11

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 3
  • Total pull requests: 3
  • Average time to close issues: 6 months
  • Average time to close pull requests: 1 minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.33
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.33
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jonrkarr (3)
Pull Request Authors
  • luciansmith (7)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 99 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 12
  • Total maintainers: 2
pypi.org: biosimulators-masspy

BioSimulators-compliant command-line interface to the MassPY simulation program <https://masspy.readthedocs.io/>.

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 99 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 11.6%
Average: 20.9%
Downloads: 21.4%
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 *
tests/requirements.txt pypi
  • biosimulators_utils * test
  • python_dateutil * test
  • pyyaml * test
.github/actions/setup-poetry-env/action.yml actions
  • actions/cache v4 composite
  • actions/setup-python v5 composite
.github/workflows/ci.yml actions
  • ./.github/actions/setup-poetry-env * composite
  • actions/cache v3 composite
  • actions/create-release v1 composite
  • ad-m/github-push-action master composite
  • codecov/codecov-action v2 composite
Dockerfile docker
  • python 3.9-slim-buster build
pyproject.toml pypi
  • flake8 ^7.1.1 develop
  • flakey ^1.0 develop
  • pytest ^8.3.3 develop
  • pytest-cov ^5.0.0 develop
  • pydata-sphinx-theme * docs
  • sphinx >=1.8 docs
  • biosimulators_utils ^0.1.151
  • cobra <= 0.23.0
  • docker ^7.1.0
  • kisao ^2.34
  • libroadrunner <= 2.2.0
  • lxml ^4.5
  • masspy ^0.1.5
  • numpy <= 1.22.0
  • python ^3.9
setup.py pypi