[](https://github.com/biosimulations/Biosimulators_MASSpy/releases)
[](https://pypi.org/project/biosimulators_masspy/)
[](https://github.com/biosimulators/Biosimulators_MASSpy/actions?query=workflow%3A%22Continuous+integration%22)
[](https://codecov.io/gh/biosimulators/Biosimulators_MASSpy)
[](#contributors-)
# BioSimulators-MASSpy
BioSimulators-compliant command-line interface to the [MASSpy](https://masspy.readthedocs.io/) 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](https://combinearchive.org/) that describe one or more simulation experiments (in [SED-ML format](https://sed-ml.org)) of one or more kinetic models in the [MASSpy schema](https://masspy.readthedocs.io/en/stable/tutorials/reading_writing_models.html) for SBML.
A list of the algorithms and algorithm parameters supported by MASSpy is available at [BioSimulators](https://biosimulators.org/simulators/masspy).
A simple web application and web service for using MASSpy to execute COMBINE/OMEX archives is also available at [runBioSimulations](https://run.biosimulations.org).
## 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 OUT_DIR, --out-dir OUT_DIR
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](LICENSE).
## Development team
This package was developed by the [Center for Reproducible Biomedical Modeling](http://reproduciblebiomodels.org) and the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York with assistance from the contributors listed [here](CONTRIBUTORS.md).
## Questions and comments
Please contact the [BioSimulators Team](mailto:info@biosimulators.org) with any questions or comments.
Raw data
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