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Open Source Science

https://github.com/biosimulations/biomodels-qc

Quality control tool for the BioModels repository of biochemical models

https://github.com/biosimulations/biomodels-qc

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.7%) to scientific vocabulary

Keywords

biomodels computational-model numerical-simulation quality-control systems-biology testing validation
Last synced: 5 months ago · JSON representation

Repository

Quality control tool for the BioModels repository of biochemical models

Basic Info
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 0
  • Open Issues: 2
  • Releases: 1
Topics
biomodels computational-model numerical-simulation quality-control systems-biology testing validation
Created almost 4 years ago · Last pushed 9 months ago
Metadata Files
Readme Contributing License Code of conduct

README.md

Latest release PyPI CI status Test coverage

BioModels-QC

Command-line application for quality controlling entries in the BioModels database and converting the primary files for entries in the database into additional formats such as BioPAX, MATLAB/Octave, and XPP.

The application can be installed locally or executed as a Docker image.

This application is intended to be used in conjuction with the best practices recommended here.

Local installation

Requirements

After installing the packages above, the following must be added to your system path: * sbfConverter.sh (Linux/Mac OS) or sbfConverter.bat (Windows) * svglint * xppaut

Installation

Run the following command to install the package. pip install biomodels-qc

Docker image

Run the following command to pull the Docker image docker pull ghcr.io/biosimulations/biomodels_qc

Tutorial

Convert the files for an entry to additional formats

Run the following command to convert the files for an entry to additional formats such as BioPAX, MATLAB/Octave, and XPP. ENTRY_DIR=/path/to/directory-for-entry biomodels-qc convert "$ENTRY_DIR"

Validate an entry

Run the following command to validate an entry of the BioModels database: ENTRY_DIR=/path/to/directory-for-entry biomodels-qc validate "$ENTRY_DIR"

Using the Docker image

Run the following commands to use the BioModels-QC Docker image to execute the same conversion and validation operations.

Convert the files for an entry to additional formats

ENTRY_DIR=/path/to/directory-for-entry\ docker run \ --mount type=bind,source="$ENTRY_DIR",target=/biomodels-entry \ --interactive \ --tty \ --rm \ ghcr.io/biosimulations/biomodels_qc \ convert \ /biomodels-entry

Validate an entry

ENTRY_DIR=/path/to/directory-for-entry CONTAINER_TEMP_DIR=$(mktemp --directory) docker run \ --mount type=bind,source="$ENTRY_DIR",target=/biomodels-entry \ --volume /var/run/docker.sock:/var/run/docker.sock \ --mount type=bind,source="$CONTAINER_TEMP_DIR",target=/tmp \ --env TEMP_DIR_HOST_PATH=$CONTAINER_TEMP_DIR \ --interactive \ --tty \ --rm \ ghcr.io/biosimulations/biomodels_qc \ validate \ /biomodels-entry

Documentation

Documentation for the command-line program is available inline.

Run the following command to obtain the help. biomodels-qc --help

Using the Docker image

Run the following command to use the BioModels-QC Docker image to obtain the help. docker run \ --interactive \ --tty \ --rm \ ghcr.io/biosimulations/biomodels_qc \ --help

API documentation

API documentation is available here.

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 and the Center for Reproducible Biomedical Modeling.

Contributing to BioModels-QC

We enthusiastically welcome contributions! Please see the guide to contributing and the developer's code of conduct.

Acknowledgements

This work was supported by National Institutes of Health award P41EB023912.

Questions and comments

Please contact the BioSimulations Team with any questions or comments.

Owner

  • Name: BioSimulations
  • Login: biosimulations
  • Kind: organization
  • Email: info@biosimulations.org
  • Location: United States of America

Enabling more comprehensive and more predictive biological models through enhanced reproducibility and reusability

GitHub Events

Total
  • Release event: 1
  • Delete event: 4
  • Issue comment event: 3
  • Push event: 17
  • Pull request event: 6
  • Create event: 2
Last Year
  • Release event: 1
  • Delete event: 4
  • Issue comment event: 3
  • Push event: 17
  • Pull request event: 6
  • Create event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 43
  • Total Committers: 3
  • Avg Commits per committer: 14.333
  • Development Distribution Score (DDS): 0.419
Past Year
  • Commits: 22
  • Committers: 1
  • Avg Commits per committer: 22.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Lucian Smith l****h@u****u 25
Jonathan Karr j****r@g****m 17
BioSimulations Daemon b****n@g****m 1
Committer Domains (Top 20 + Academic)
uw.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 10
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 day
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.1
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 day
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • luciansmith (1)
Pull Request Authors
  • luciansmith (10)
  • bilalshaikh42 (1)
  • renovate[bot] (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 65 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
  • Total maintainers: 3
pypi.org: biomodels-qc

Utility functions to assist biomodels curation.

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 65 Last month
Rankings
Dependent packages count: 7.3%
Dependent repos count: 22.1%
Average: 27.7%
Forks count: 30.0%
Stargazers count: 38.9%
Downloads: 40.1%
Maintainers (3)
lpsmith biosimulations jcschaff
Last synced: 6 months ago

Dependencies

docs-src/requirements.txt pypi
  • sphinx >=1.8
  • sphinxprettysearchresults *
requirements.txt pypi
  • biosimulators_utils >=0.1.171
  • cement *
  • kisao *
  • lxml *
  • nbformat *
  • owlready2 *
  • pypdf2 *
  • python_copasi *
  • python_dateutil *
  • python_libsbml *
  • scipy *
  • termcolor *
  • xmldiff *
tests/requirements.txt pypi
  • capturer * test
  • pytest * test
  • pytest_cov * test
.github/workflows/ci.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/create-release v1 composite
  • actions/setup-java v2 composite
  • actions/setup-node v2 composite
  • actions/setup-python v2 composite
  • ad-m/github-push-action master composite
  • codecov/codecov-action v2 composite
  • whoan/docker-build-with-cache-action v5 composite
Dockerfile docker
  • python 3.9-slim-buster build
setup.py pypi