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توضیحات

BioSimulators-compliant command-line interface to the jNeuroML/pyNeuroML, NEURON, and NetPyNe simulation programs.

ویژگی	مقدار
سیستم عامل	-
نام فایل	biosimulators-pyneuroml-0.0.9
نام	biosimulators-pyneuroml
نسخه کتابخانه	0.0.9
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	BioSimulators Team
ایمیل نویسنده	info@biosimulators.org
آدرس صفحه اصلی	https://github.com/biosimulators/Biosimulators_pyNeuroML
آدرس اینترنتی	https://pypi.org/project/biosimulators-pyneuroml/
مجوز	MIT

|Latest release| |PyPI| |CI status| |Test coverage| |All Contributors| BioSimulators-pyNeuroML ======================= BioSimulators-compliant command-line interfaces and Docker images for the `jNeuroML <https://github.com/NeuroML/jNeuroML>`__/`pyNeuroML <https://github.com/NeuroML/pyNeuroML>`__, `NEURON <https://neuron.yale.edu/>`__, `NetPyNe <http://netpyne.org/>`__, and simulation programs. These command-line interfaces and Docker images enable users to use jNeuroML/pyNeuroML, NEURON, and NetPyNe 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 models (in `NeuroML <https://neuroml.org/>`__/`LEMS <https://lems.github.io/LEMS/>`__ format). A list of the algorithms and algorithm parameters supported by jNeuroML/pyNeuroML, NEURON, and NetPyNe is available at `BioSimulators <https://biosimulators.org/simulators/pyneuroml>`__. A simple web application and web service for using jNeuroML/pyNeuroML, NEURON, and NetPyNe to execute COMBINE/OMEX archives is also available at `runBioSimulations <https://run.biosimulations.org>`__. Installation ------------ Install Python package ~~~~~~~~~~~~~~~~~~~~~~ 1. Install Java 2. Install this package :: pip install biosimulators-pyneuroml 3. To install support for NetPyNe, install NEURON and install this package with the ``netpyne`` option: :: pip install biosimulators-pyneuroml 4. To install support for NEURON, install NEURON and install this package with the ``neuron`` option: :: pip install biosimulators-pyneuroml Install Docker image ~~~~~~~~~~~~~~~~~~~~ This package provides three Docker images: :: docker pull ghcr.io/biosimulators/netpyne docker pull ghcr.io/biosimulators/neuron docker pull ghcr.io/biosimulators/pyneuroml Usage ----- Local usage ~~~~~~~~~~~ This package provides three command-line applications, each with the interface illustrated below. - ``biosimulators-neuron`` - ``biosimulators-netpyne`` - ``biosimulators-pyneuroml`` :: usage: 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 exit Usage through Docker containers ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The 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.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/pyneuroml:latest \ -i /root/in/modeling-study.omex \ -o /root/out Documentation ------------- Documentation is available at https://docs.biosimulators.org/Biosimulators_pyNeuroML/. License ------- This package is released under the `MIT <LICENSE>`__. Development team ---------------- This package was developed by the `Karr Lab <https://www.karrlab.org>`__ at the Icahn School of Medicine at Mount Sinai and the `Center for Reproducible Biomedical Modeling <https://reproduciblebiomodels.org/>`__ 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. .. |Latest release| image:: https://img.shields.io/github/v/tag/biosimulators/Biosimulators_pyNeuroML :target: https://github.com/biosimulations/Biosimulators_pyNeuroML/releases .. |PyPI| image:: https://img.shields.io/pypi/v/biosimulators_pyneuroml :target: https://pypi.org/project/biosimulators_pyneuroml/ .. |CI status| image:: https://github.com/biosimulators/Biosimulators_pyNeuroML/workflows/Continuous%20integration/badge.svg :target: https://github.com/biosimulators/Biosimulators_pyNeuroML/actions?query=workflow%3A%22Continuous+integration%22 .. |Test coverage| image:: https://codecov.io/gh/biosimulators/Biosimulators_pyNeuroML/branch/dev/graph/badge.svg :target: https://codecov.io/gh/biosimulators/Biosimulators_pyNeuroML .. |All Contributors| image:: https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_pyNeuroML/HEAD :target: #contributors-

نیازمندی

مقدار	نام
>=0.1.147	biosimulators-utils[lems,logging,neuroml]
-	kisao
-	lxml
<=1.0.0.2	netpyne
-	numpy
-	psutil
>=0.5.20	pyneuroml
-	biosimulators-utils[containers]
-	brian2
-	netpyne
-	neuron
-	parameterized
-	python-dateutil
-	brian2
-	netpyne
-	neuron
-	neuron
-	biosimulators-utils[containers]
-	parameterized
-	python-dateutil

نحوه نصب

نصب پکیج whl biosimulators-pyneuroml-0.0.9:

pip install biosimulators-pyneuroml-0.0.9.whl

نصب پکیج tar.gz biosimulators-pyneuroml-0.0.9:

pip install biosimulators-pyneuroml-0.0.9.tar.gz