Comments (1)
After doing some deep diving, I have mapped out the general schema for the container which is created by the Dockerfile within this repo using a JSON-like object. The schema is:
{
"base_image": "python:3.9-slim-buster",
"version": "0.1.35",
"software": "COPASI",
"software.version": "4.36.260",
"about": {
"summary": "Open-source software package for the simulation and analysis of biochemical networks and their dynamics.",
"home": "http://copasi.org/",
"documentation": "http://copasi.org/Support/User_Manual/",
"license_file": "https://github.com/copasi/COPASI/blob/develop/license.txt",
"license": "SPDX:Artistic-2.0",
"tags": "kinetic modeling,dynamical simulation,systems biology,biochemical networks,SBML,SED-ML,COMBINE,OMEX,BioSimulators"
},
"org.opencontainers.image.title": "COPASI",
"org.opencontainers.image.version": "4.36.260",
"org.opencontainers.image.description": "Open-source software package for the simulation and analysis of biochemical networks and their dynamics.",
"org.opencontainers.image.url": "http://copasi.org/",
"org.opencontainers.image.documentation": "http://copasi.org/Support/User_Manual/",
"org.opencontainers.image.source": "https://github.com/biosimulators/Biosimulators_COPASI",
"org.opencontainers.image.authors": "BioSimulators Team [email protected]",
"org.opencontainers.image.vendor": "BioSimulators Team",
"org.opencontainers.image.licenses": "Artistic-2.0",
"maintainer": "BioSimulators Team [email protected]",
"dependencies": [
"libfreetype6"
],
"entrypoint": [
"biosimulators-copasi"
],
"cmd": [],
"environment": {
"ALGORITHM_SUBSTITUTION_POLICY": "SIMILAR_VARIABLES",
"VERBOSE": "0",
"MPLBACKEND": "PDF"
}
}
May this serve as a mapping for Dockerfile traversal.
from biosimulators_copasi.
Related Issues (20)
- Apply new KISAO terms for algorithms and parameters HOT 2
- Add citation for Stochastic Runge-Kutta Method HOT 1
- What are the user-configurable parameters of the hybrid LSODA algorithm? HOT 1
- Support hybrid RK45 method HOT 2
- Improve messages for COPASI errors HOT 2
- Expose static and steady-state analyses through SED-ML HOT 1
- Get values of non-constant parameters HOT 8
- Mark Steady State Simulations / Scan as supported HOT 3
- Internalize functionality into COPASI itself (obviating the need for this repository) HOT 7
- Setup cron job to pull COPASI releases from PyPi HOT 1
- Substitute algorithm when Radau5 requested for model with events HOT 1
- Substitute hybrid runge kutta and LSODA methods to hybrid RK-45 for models with events HOT 1
- copasi_model_obj_common_name needs to be a string HOT 4
- biosimulators no longer working on macOS HOT 4
- Lowering Cognitive complexity as per SonarCloud
- Documentation discrepancies between repo and website. HOT 1
- Incorrectly raised Exception regarding number of time points HOT 1
- Biosimulators copasi gives incorrect results that normal copasi doesn't HOT 3
- All biomodels Copasi currently fails for
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from biosimulators_copasi.