https://github.com/biosimulators/biosimulators_amici
AMICI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
Science Score: 13.0%
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○CITATION.cff file
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○Scientific vocabulary similarity
Low similarity (15.8%) to scientific vocabulary
Keywords
Repository
AMICI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
Basic Info
- Host: GitHub
- Owner: biosimulators
- License: mit
- Language: Python
- Default Branch: dev
- Homepage: https://docs.biosimulators.org/Biosimulators_AMICI
- Size: 2.5 MB
Statistics
- Stars: 3
- Watchers: 4
- Forks: 1
- Open Issues: 4
- Releases: 29
Topics
Metadata Files
README.md
BioSimulators-AMICI
BioSimulators-compliant command-line interface to the AMICI simulation program.
This command-line interface and Docker image enable users to use AMICI 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 AMICI is available at BioSimulators.
A simple web application and web service for using AMICI to execute COMBINE/OMEX archives is also available at runBioSimulations.
Installation
Dependencies
- Python >= 3.7
- pip
- libatlas
- g++
- swig
Install Python package
pip install biosimulators-amici
Install Docker image
docker pull ghcr.io/biosimulators/amici
Usage
Local usage
``` usage: biosimulators-amici [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
BioSimulators-compliant command-line interface to the AMICI simulation program https://github.com/AMICI-dev/AMICI.
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/amici:latest \
-i /root/in/modeling-study.omex \
-o /root/out
Documentation
Documentation is available at https://docs.biosimulators.org/Biosimulators_AMICI/.
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
- Website: https://biosimulators.org
- Twitter: BioSimulators
- Repositories: 20
- Profile: https://github.com/biosimulators
Enabling more comprehensive and more predictive biological models through standardized simulation tools
GitHub Events
Total
Last Year
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 147
- Total Committers: 2
- Avg Commits per committer: 73.5
- Development Distribution Score (DDS): 0.245
Top Committers
| Name | Commits | |
|---|---|---|
| Jonathan Karr | j****r@g****m | 111 |
| biosimulatorsdaemon | b****n@g****m | 36 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 7
- Total pull requests: 4
- Average time to close issues: 23 days
- Average time to close pull requests: about 6 hours
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 2.14
- Average comments per pull request: 0.0
- Merged pull requests: 4
- 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
Top Authors
Issue Authors
- jonrkarr (3)
- luciansmith (2)
- dweindl (1)
- AlexPatrie (1)
Pull Request Authors
- luciansmith (2)
- jonrkarr (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 166 last-month
- Total dependent packages: 0
- Total dependent repositories: 2
- Total versions: 29
- Total maintainers: 2
pypi.org: biosimulators-amici
BioSimulators-compliant command-line interface to the AMICI simulation program <https://github.com/AMICI-dev/amici>.
- Homepage: https://github.com/biosimulators/Biosimulators_AMICI>
- Documentation: https://biosimulators-amici.readthedocs.io/
- License: MIT
-
Latest release: 0.1.24
published over 2 years ago
Rankings
Maintainers (2)
Dependencies
- pydata-sphinx-theme *
- sphinx >=1.8
- sphinxprettysearchresults *
- amici >=0.11.17
- biosimulators_utils >=0.1.151
- kisao *
- lxml *
- numpy *
- sympy >=1.7
- biosimulators_utils * test
- python_dateutil * test
- actions/cache v3 composite
- actions/create-release v1 composite
- actions/setup-python v3 composite
- ad-m/github-push-action master composite
- codecov/codecov-action v2 composite
- python 3.11-slim-bookworm build