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 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/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.
2 maintainers
Metadata
2 maintainers
Release files for biosimulators-pysces 0.1.33
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| biosimulators_pysces-0.1.33.tar.gz | 16.4 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| biosimulators_pysces-0.1.33-py2.py3-none-any.whl | Python 3, Python 2 | none | any | Details |
Total release size: 27.4 kB
Release files / biosimulators_pysces-0.1.33.tar.gz
| Download URL | biosimulators_pysces-0.1.33.tar.gz |
|---|---|
| Size | 16.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
a83afae594cdfed72a0d27ba0f389210370813d5b176730283613f895f1270ff
|
|
BLAKE2b-256 checksum How to use checksums |
e32ca6fd81351e8a883556ebcd76f208080a2ea66a5ac6380a9f2f28de7be0e7
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.10.15
|
Release files / biosimulators_pysces-0.1.33-py2.py3-none-any.whl
| Download URL | biosimulators_pysces-0.1.33-py2.py3-none-any.whl |
|---|---|
| Size | 10.9 kB |
| Tags | Python 2 Python 3 |
|
SHA-256 checksum How to use checksums |
909bcf22f5b9301487016a313e79b3d7b15ecf6346f9a89192be22fd5407ebcb
|
|
BLAKE2b-256 checksum How to use checksums |
bbb6de7080cb839cf063ae17464b858ac74f24a273d46dba901cbdca356dbe94
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.10.15
|
