Saravanan666/pypi-org huggingface dataset:
Package: biosimulators-amici
BioSimulators-AMICIBioSimulators-compliant command-line interface to theAMICIsimulation program.This command-line interface and Docker image enable users to use AMICI
to executeCOMBINE/OMEX archivesthat
describe one or more simulation experiments (inSED-ML
format) of one or more models (inSBML
format).A list of the algorithms and algorithm parameters supported by AMICI is
available atBioSimulators.A simple web application and web service for using AMICI to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationDependenciesPython >= 3.7piplibatlasg++swigInstall Python packagepip install biosimulators-amiciInstall Docker imagedocker pull ghcr.io/biosimulators/amiciUsageLocal usageusage: 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 OUT_DIR, --out-dir OUT_DIR
                        Directory to save outputs
  -v, --version         show program's version number and exitUsage through Docker containerThe 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.omexand 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/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_AMICI/.LicenseThis package is released under theMIT license.Development teamThis package was developed by theCenter for Reproducible Biomedical
Modelingand theKarr
Labat the Icahn School of Medicine at
Mount Sinai in New York with assistance from the contributors listedhere.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments.
Package: biosimulators-bionetgen
BioSimulators-BioNetGenBioSimulators-compliant command-line interface and Docker image for theBioNetGensimulation program.This command-line interface and Docker image enable users to use
BioNetGen to executeCOMBINE/OMEX
archivesthat describe one or more
simulation experiments (inSED-ML format) of
one or more models (inBNGL format).A list of the algorithms and algorithm parameters supported by BioNetGen
is available atBioSimulators.A simple web application and web service for using BioNetGen to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationInstall Python packageAfter installing BioNetGen, use pip to install this package as
illustrated below.pip install biosimulators-bionetgenInstall Docker imagedocker pull ghcr.io/biosimulators/bionetgenUsageLocal usageusage: bionetgen [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>.

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 exitUsage through Docker containerThe 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.omexand 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/bionetgen:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_BioNetGen/.LicenseThis package is released under theMIT license.Development teamThis package was developed by theKarr Labat the Icahn School of Medicine at Mount Sinai,Ali Sinan
Saglamin the Faeder Lab at the University of Pittsburgh, and theCenter for
Reproducible Biomedical Modelingwith assistance from the contributors listedhere.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments
about the command-line program or Docker image. Please contactAli
Sinan Saglamwith any questions or comments
about BioNetGen.
Package: biosimulators-boolnet
BioSimulators-BoolNetBioSimulators-compliant command-line interface to theBoolNetsimulation
program.This command-line interface and Docker image enable users to use BoolNet
to executeCOMBINE/OMEX archivesthat
describe one or more simulation experiments (inSED-ML
format) of one or more logical models (inSBML-qual format).A list of the algorithms and algorithm parameters supported by BoolNet
is available atBioSimulators.A simple web application and web service for using BoolNet to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationInstall Python packagepip install biosimulators-boolnetInstall Docker imagedocker pull ghcr.io/biosimulators/boolnetUsageLocal usageusage: biosimulators-boolnet [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the BoolNet simulation program <https://sysbio.uni-ulm.de/?Software:BoolNet>.

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 exitUsage through Docker containerThe 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.omexand 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/boolnet:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_BoolNet/.LicenseThis package is released under theMIT license.Development teamThis package was developed by theCenter for Reproducible Biomedical
Modelingand theKarr
Labat the Icahn School of Medicine at
Mount Sinai in New York with assistance from the contributors listedhere.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments.
Package: biosimulators-cbmpy
BioSimulators-CBMPyBioSimulators-compliant command-line interface to theCBMPysimulation program.This command-line interface and Docker image enable users to use CBMPy
to executeCOMBINE/OMEX archivesthat
describe one or more simulation experiments (inSED-ML
format) of one or more models (inSBML
format).A list of the algorithms and algorithm parameters supported by CBMPy is
available atBioSimulators.A simple web application and web service for using CBMPy to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationInstall Python packagepip install biosimulators-cbmpyInstall Docker imagedocker pull ghcr.io/biosimulators/cbmpyUsageLocal usageusage: biosimulators-cbmpy [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the CBMPy simulation program <http://cbmpy.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 exitUsage through Docker containerThe 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.omexand 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/cbmpy:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_CBMPy/.LicenseThis package is released under theMIT license.Development teamThis package was developed by theCenter for Reproducible Biomedical
Modelingand theKarr
Labat the Icahn School of Medicine at
Mount Sinai in New York with assistance from the contributors listedhere.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments.
Package: biosimulators-cobrapy
BioSimulators-COBRApyBioSimulators-compliant command-line interface and Docker image for theCOBRApysimulation program.This command-line interface and Docker image enable users to use COBRApy
to executeCOMBINE/OMEX archivesthat
describe one or more simulation experiments (inSED-ML
format) of one or more models (inSBML
format).A list of the algorithms and algorithm parameters supported by COBRApy
is available atBioSimulators.A simple web application and web service for using COBRApy to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationInstall Python packagepip install biosimulators-cobrapyInstall Docker imagedocker pull ghcr.io/biosimulators/cobrapyUsageSED-ML targets for simulation predictionsBioSimulators-COBRApy recognizes the following targets for simulation
predictions:FBA (KISAO_0000437), parsimonious FBA (KISAO_0000528),
geometric FBA (KISAO_0000527):Objective:fbc:objective/@valueReaction flux:sbml:reaction/@fluxReaction reduced cost:sbml:reaction/@reducedCostSpecies shadow price:sbml:species/@shadowPriceFVA (KISAO_0000526):Minimum reaction flux:sbml:reaction/@minFluxMaximum reaction flux:sbml:reaction/@maxFluxPlease seehttps://docs.biosimulations.orgfor more information.Local usageusage: biosimulators-cobrapy [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.

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 exitUsage through Docker containerThe 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.omexand 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/cobrapy:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_COBRApy/.LicenseThis package is released under theMIT license.Development teamThis package was developed by theCenter for Reproducible Biomedical
Modelingand theKarr
Labat the Icahn School of Medicine at
Mount Sinai with assistance from the contributors listedhere.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments.
Package: biosimulators-copasi
BioSimulators-COPASIBioSimulators-compliant command-line interface and Docker image for theCOPASIsimulation program.This command-line interface and Docker image enable users to use COPASI
to executeCOMBINE/OMEX archivesthat
describe one or more simulation experiments (inSED-ML
format) of one or more models (inSBML
format).A list of the algorithms and algorithm parameters supported by COPASI is
available atBioSimulators.A simple web application and web service for using COPASI to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationInstall Python packagepip install biosimulators-copasiInstall Docker imagedocker pull ghcr.io/biosimulators/copasiUsageLocal usageusage: biosimulators-copasi [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the COPASI simulation program <http://copasi.org>.

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 exitUsage through Docker containerThe 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.omexand 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/copasi:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_COPASI/.LicenseThis package is released under theMIT license. COPASI is
released under theArtistic 2.0
License.Development teamThis package was developed by theCenter for Reproducible Biomedical
Modeling. COPASI was developed by
ateamat the University of
Connecticut, the University of Heidelberg, and the University of
Virginia with assistance from the contributors listedhere.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments.
Package: biosimulators-gillespy2
BioSimulators-GillesPy2BioSimulators-compliant command-line interface and Docker image for theGillesPy2simulation program.This command-line interface and Docker image enable users to use
GillesPy2 to executeCOMBINE/OMEX
archivesthat describe one or more
simulation experiments (inSED-ML format) of
one or more models (inSBML format).A list of the algorithms and algorithm parameters supported by GillesPy2
is available atBioSimulators.A simple web application and web service for using GillesPy2 to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationDependenciesPython >= 3.7pipbuild-essentialInstall Python packagepip install biosimulators-gillespy2Install Docker imagedocker pull ghcr.io/biosimulators/gillespy2UsageLocal usageusage: biosimulators-gillespy2 [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the GillesPy2 <https://stochss.github.io/GillesPy2> simulation program.

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 exitUsage through Docker containerThe 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.omexand 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/gillespy2:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_GillesPy2/.LicenseThis package is released under theMIT.Development teamThis package was developed by theKarr Labat the Icahn School of Medicine at Mount Sinai and theCenter for
Reproducible Biomedical Modelingwith assistance from the contributors listedhere.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments.
Package: biosimulators-ginsim
BioSimulators-GINsimBioSimulators-compliant command-line interface to theGINsimsimulation program.This command-line interface and Docker image enable users to use GINsim
to executeCOMBINE/OMEX archivesthat
describe one or more simulation experiments (inSED-ML
format) of one or more logical models (inSBML-qualor GINsim’s formats).A list of the algorithms and algorithm parameters supported by GINsim is
available atBioSimulators.A simple web application and web service for using GINsim to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationInstall Python packageInstall Java, Python, and pipInstall theGINsim Python
packageInstall this packagepip install biosimulators-ginsimInstall Docker imagedocker pull ghcr.io/biosimulators/ginsimUsageLocal usageusage: biosimulators-ginsim [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the GINsim simulation program <http://ginsim.org/>.

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 exitUsage through Docker containerThe 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.omexand 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/ginsim:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_GINsim/.LicenseThis package is released under theMIT license.Development teamThis package was developed by theCenter for Reproducible Biomedical
Modelingand theKarr
Labat the Icahn School of Medicine at
Mount Sinai in New York with assistance from the contributors listedhere.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments.
Package: biosimulators-libsbmlsim
BioSimulators-LibSBMLSimBioSimulators-compliant command-line interface to theLibSBMLSimsimulation program.This command-line interface and Docker image enable users to use
LibSBMLSim to executeCOMBINE/OMEX
archivesthat describe one or more
simulation experiments (inSED-ML format) of
one or more kinetic models in SBML format.A list of the algorithms and algorithm parameters supported by
LibSBMLSim is available atBioSimulators.A simple web application and web service for using LibSBMLSim to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationInstall Python packageInstallLibSBMLSimInstall this packagepip install biosimulators-libsbmlsimInstall Docker imagedocker pull ghcr.io/biosimulators/libsbmlsimUsageLocal usageusage: biosimulators-libsbmlsim [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the LibSBMLSim simulation program <https://fun.bio.keio.ac.jp/software/libsbmlsim/>.

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 exitUsage through Docker containerThe 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.omexand 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/libsbmlsim:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/.LicenseThis package is released under theMIT license.Development teamThis package was developed by theCenter for Reproducible Biomedical
Modelingand theKarr
Labat the Icahn School of Medicine at
Mount Sinai in New York with assistance from the contributors listedhere.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments.