Saravanan666/pypi-org huggingface dataset:
Package: biosimulators-masspy
BioSimulators-MASSpyBioSimulators-compliant command-line interface to theMASSpysimulation program for
kinetic simulations of metabolic reaction networks.This command-line interface and Docker image enable users to use MASSpy
to executeCOMBINE/OMEX archivesthat
describe one or more simulation experiments (inSED-ML
format) of one or more kinetic models in theMASSpy
schemafor SBML.A list of the algorithms and algorithm parameters supported by MASSpy is
available atBioSimulators.A simple web application and web service for using MASSpy to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationDependenciesPython >= 3.7piplibncurseslibxmlInstall Python packagepip install biosimulators-masspyInstall Docker imagedocker pull ghcr.io/biosimulators/masspyUsageLocal usageusage: 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 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/masspy:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_MASSpy/.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-opencor
BioSimulators-OpenCORBioSimulators-compliant command-line interface and Docker image for theOpenCORsimulation program.This command-line interface and Docker image enable users to use OpenCOR
to executeCOMBINE/OMEX archivesthat
describe one or more simulation experiments (inSED-ML
format) of one or more models (inCellML
format).A list of the algorithms and algorithm parameters supported by OpenCOR
is available atBioSimulators.A simple web application and web service for using OpenCOR to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationInstall Python package and command-line applicationInstall the requirements for OpenCOR:apt-getinstall-y\curl\libpulse-mainloop-glib0\libx11-6\libxext6\libxslt1.1\sqlite3InstallOpenCOR:url=https://opencor.ws/downloads/snapshots/2021-05-19/OpenCOR-2021-05-19-Linux.tar.gzcurl$url|tar-xz--directory=/opt/Add OpenCOR to your system path:exportPATH=/opt/OpenCOR-2021-05-19-Linux:$PATHInstall pip for this version of Python:curlhttps://bootstrap.pypa.io/get-pip.py|OpenCOR-cPythonShellUse pip to install this package:/opt/OpenCOR-2021-05-19-Linux/python/bin/python-mpipinstallbiosimulators-opencorInstall Docker imagedocker pull ghcr.io/biosimulators/opencorUsageLocal usageusage: opencor [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the OpenCOR <https://opencor.ws> 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/opencor:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_OpenCOR/.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-pyneuroml
BioSimulators-pyNeuroMLBioSimulators-compliant command-line interfaces and Docker images for
thejNeuroML/pyNeuroML,NEURON,NetPyNe, and simulation programs.These command-line interfaces and Docker images enable users to use
jNeuroML/pyNeuroML, NEURON, and NetPyNe to executeCOMBINE/OMEX
archivesthat describe one or more
simulation experiments (inSED-ML format) of
one or more models (inNeuroML/LEMSformat).A list of the algorithms and algorithm parameters supported by
jNeuroML/pyNeuroML, NEURON, and NetPyNe is available atBioSimulators.A simple web application and web service for using jNeuroML/pyNeuroML,
NEURON, and NetPyNe to execute COMBINE/OMEX archives is also available
atrunBioSimulations.InstallationInstall Python packageInstall JavaInstall this packagepip install biosimulators-pyneuromlTo install support for NetPyNe, install NEURON and install this
package with thenetpyneoption:pip install biosimulators-pyneuromlTo install support for NEURON, install NEURON and install this
package with theneuronoption:pip install biosimulators-pyneuromlInstall Docker imageThis package provides three Docker images:docker pull ghcr.io/biosimulators/netpyne
docker pull ghcr.io/biosimulators/neuron
docker pull ghcr.io/biosimulators/pyneuromlUsageLocal usageThis package provides three command-line applications, each with the
interface illustrated below.biosimulators-neuronbiosimulators-netpynebiosimulators-pyneuromlusage: biosimulators-pyneuroml [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the pyNeuroML <https://github.com/NeuroML/pyNeuroML> 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 containersThe entrypoints to the Docker images support 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/pyneuroml:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_pyNeuroML/.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-pysces
BioSimulators-PySCeSBioSimulators-compliant command-line interface to thePySCeSsimulation program.This command-line interface and Docker image enable users to use PySCeS
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 PySCeS is
available atBioSimulators.A simple web application and web service for using PySCeS to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationInstall Python packagepip install biosimulators-pyscesInstall Docker imagedocker pull ghcr.io/biosimulators/pyscesUsageLocal usageusage: 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 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/pysces:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_PySCeS/.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-tellurium
BioSimulators-telluriumBioSimulators-compliant command-line interface and Docker image for thetelluriumsimulation program.This command-line interface and Docker image enable users to use
tellurium 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 tellurium
is available atBioSimulators.A simple web application and web service for using tellurium to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationDependenciesPythonpiplibncurseslibxmlInstall Python packagepip install biosimulators-telluriumInstall Docker imagedocker pull ghcr.io/biosimulators/telluriumUsageLocal usageusage: biosimulators-tellurium [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the tellurium simulation program <http://tellurium.analogmachine.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/tellurium:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_tellurium/.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-test-suite
BioSimulators test suiteThe BioSimulators test suite is a tool for validating that biosimulation
software tools implement theBioSimulators conventions for
biosimulation
tools.The test suite is composed of two parts:A collection of example modeling projects. Each
project is represented by a singleCOMBINE/OMEX
archivethat contains one or more
simulation experiments described using theSimulation Experiment
Description Markup Language (SED-ML)and one
or more models described using a format such as theBioNetGen
Language (BNGL)or theSystems Biology
Markup Language (SBML).Software for checking that biosimulation tools execute these projects
according to the BioSimulators conventions.Simulation tools support theBioSimulators standard command-line
arguments.Simulation tools support theBioSimulators conventions for Docker
images.Simulation tools follow theBioSimulators conventions for
executing simulations described by SED-ML files in COMBINE/OMEX
archives.Simulation tools support theBioSimulators conventions for the
outputs of SED-ML files in COMBINE/OMEX
archives.Installation instructions, tutorial, and API documentationInstallation instructions, tutorial, and API documentation are availablehere.LicenseThe software in this package is released under theMIT
License. The modeling projects in this package are released
under theCreative Commons 1.0 Universal (CC0)
license.Development teamThis package was developed by theKarr Labat the Icahn School of Medicine at Mount Sinai in New York, thehttps://health.uconn.edu/cell-analysis-modeling/at the University of Connecticut, and theCenter for Reproducible
Biomedical Modelingwith
assistance from the contributors listedhere.Contributing to the test suiteWe enthusiastically welcome contributions to the test suite! Please see
theguide to contributingand thedeveloper’s
code of conduct.AcknowledgementsThis work was supported by National Institutes of Health award
P41EB023912.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments.
Package: biosimulators-xpp
BioSimulators-XPPBioSimulators-compliant command-line interface to theXPPsimulation
program.This command-line interface and Docker image enable users to use XPP to
executeCOMBINE/OMEX archivesthat
describe one or more simulation experiments (inSED-ML
format) of one or more kinetic models in XPP
format.A list of the algorithms and algorithm parameters supported by XPP is
available atBioSimulators.A simple web application and web service for using XPP to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationInstall Python packageInstallXPPInstall this packagepip install biosimulators-xppInstall Docker imagedocker pull ghcr.io/biosimulators/xppUsageLocal usageusage: biosimulators-xpp [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the XPP simulation program <http://www.math.pitt.edu/~bard/xpp/xpp.html>.

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/xpp:latest \
    -i /root/in/modeling-study.omex \
    -o /root/outDocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_XPP/.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: biosmoother
BioSmoother performs on-the-fly analysis and visualization (filtering, normalization, downstream processing, and displaying) of interactome data (https://en.wikipedia.org/wiki/Chromosome_conformation_capture). See the GitHub repository for more information:https://github.com/Siegel-Lab/BioSmoother.BioSmoother’s documentation is available athttps://biosmoother.rtfd.io/.
Package: biosniff
Python version:3.7, 3.8, 3.9, 3.10Issues:On githubThis tools is a simple Sniffer for Biological formats (and compression formats)Installationpip install biosniffUsagebiosniff file.fasta
biosniff example.vcf
...There are about 50 formats supported for now including:abi, bam, bai, bcf, binary_bed, bed, bedgraph, bigwig, bigbed, bplink,
bz2, cram, clustal, dsrc, embl,ena, fasta, fastq, genbank, gfa, gff2,
gff3, gz, json, maf, newick, nexus, ods, paf, phylip, phyloxml, plink,
qual, sam, scf, stockholm, rar, twobit, tsv, vcf, wiggle, wig,
xls, xlsx, xmfa, yaml, zip, 7zip, xzChangelogVersionDescription1.0.0add logo, add Python 3.10 in CI and tag to version 1.00.4.0additional test and fix missing click requirements0.3.0add missing MANIFEST and applied black0.2.0more tests (80% coverage) and some simplifications0.1.0first commit
Package: biosphere
BiosphereSimple, fast random forests.Random forests with a runtime ofO(n d log(n) + n_estimators d n max_depth)instead ofO(n_estimators mtry n log(n) max_depth).biosphereis available as a rust crate and as a Python package.BenchmarksRan on an M1 Pro withn_jobs=4. Wall-time to fit a Random Forest including OOB score with 400 trees to
theNYC Taxi dataset,
minimum over 10 runs. After feature engineering, the dataset consists of 5 numerical and 7 one-hot encoded
features.model100020004000800016000320006400012800025600051200010240002048000biosphere0.04s0.08s0.15s0.32s0.65s1.40s2.97s6.48s15.53s37.91s96.69s231.82sscikit-learn0.28s0.34s0.46s0.69s1.23s2.47s4.99s10.49s22.11s51.04s118.95s271.03s
Package: bios-pnp
Very simple module that enumerates Legacy Plug and Play devices.Currently only Linux is supported. The data is sourced from the sysfs
file system.Example:>>> from bios_pnp import pnp
>>> print(list(pnp.get_all_pnp_devices_from_sysfs()))
[Device(ids=[DeviceId(vendor=PNP, product=0x0b0, revision=0x0)])]LicenseApache 2.0
Package: biosppy
🌀 New module for signal quality assessment 🌀
With the signals.quality module you can now evaluate the quality of your signals!
So far, the EDA and ECG quality are available, but more could be added soon.🫀 New module for heart rate variability 🫀
With the signals.hrv module you can now extract HRV features. Check it out! (PR #19)✨ New plotting design ✨
New colors, new style and new features, check it out!🎊 New module for feature extraction 🎊
With the 'features' module you can easily extract features from your biosignals!
(Check PR #4)BioSPPy - Biosignal Processing in PythonA toolbox for biosignal processing written in Python.The toolbox bundles together various signal processing and pattern recognition
methods geared towards the analysis of biosignals.Highlights:Support for various biosignals: BVP, ECG, EDA, EEG, EMG, PCG, PPG, RespirationSignal analysis primitives: filtering, frequency analysisClusteringBiometricsDocumentation can be found at:http://biosppy.readthedocs.org/InstallationInstallation can be easily done withpip:$pipinstallbiosppyAlternatively, you can install the latest version from the GitHub repository:$pipinstallgit+https://github.com/scientisst/BioSPPy.gitSimple ExampleThe code below loads an ECG signal from theexamplesfolder, filters it,
performs R-peak detection, and computes the instantaneous heart rate.frombiosppyimportstoragefrombiosppy.signalsimportecg# load raw ECG signalsignal,mdata=storage.load_txt('./examples/ecg.txt')# process it and plotout=ecg.ecg(signal=signal,sampling_rate=1000.,show=True)This should produce a plot similar to the one below.Dependenciesbidicth5pymatplotlibnumpyscikit-learnscipyshortuuidsixjoblibCitingPlease use the following if you need to cite BioSPPy:Carreiras C, Alves AP, Lourenço A, Canento F, Silva H, Fred A,et al.BioSPPy - Biosignal Processing in Python, 2015-,https://github.com/PIA-Group/BioSPPy/[Online; accessed<year>-<month>-<day>].@Misc{,
  author ={Carlos Carreiras and Ana Priscila Alves and Andr\'{e}Louren\c{c}o and Filipe Canento and Hugo Silva and Ana Fred and others},
  title ={{BioSPPy}: Biosignal Processing in{Python}},
  year ={2015--},
  url = "https://github.com/PIA-Group/BioSPPy/",
  note ={[Online; accessed <today>]}}LicenseBioSPPy is released under the BSD 3-clause license. See LICENSE for more details.DisclaimerThis program is distributed in the hope it will be useful and provided
to you "as is", but WITHOUT ANY WARRANTY, without even the implied
warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This
program is NOT intended for medical diagnosis. We expressly disclaim any
liability whatsoever for any direct, indirect, consequential, incidental
or special damages, including, without limitation, lost revenues, lost
profits, losses resulting from business interruption or loss of data,
regardless of the form of action or legal theory under which the
liability may be asserted, even if advised of the possibility of such
damages.