# pyNeuroML **Repository Path**: forwardinglei/pyNeuroML ## Basic Information - **Project Name**: pyNeuroML - **Description**: No description available - **Primary Language**: Python - **License**: LGPL-3.0 - **Default Branch**: master - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2025-02-20 - **Last Updated**: 2025-02-20 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README pyNeuroML ========= [![GitHub CI](https://github.com/NeuroML/pyNeuroML/actions/workflows/ci.yml/badge.svg)](https://github.com/NeuroML/pyNeuroML/actions/workflows/ci.yml) [![PyPI](https://img.shields.io/pypi/v/pyNeuroML)](https://pypi.org/project/pyNeuroML/) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyNeuroML)](https://pypi.org/project/pyNeuroML/) [![GitHub](https://img.shields.io/github/license/NeuroML/pyNeuroML)](https://github.com/NeuroML/pyNeuroML/blob/master/LICENSE.lesser) [![GitHub pull requests](https://img.shields.io/github/issues-pr/NeuroML/pyNeuroML)](https://github.com/NeuroML/pyNeuroML/pulls) [![GitHub issues](https://img.shields.io/github/issues/NeuroML/pyNeuroML)](https://github.com/NeuroML/pyNeuroML/issues) [![Documentation Status](https://readthedocs.org/projects/pyneuroml/badge/?version=latest)](https://pyneuroml.readthedocs.io/en/latest/?badge=latest) [![GitHub Org's stars](https://img.shields.io/github/stars/NeuroML?style=social)](https://github.com/NeuroML) [![Twitter Follow](https://img.shields.io/twitter/follow/NeuroML?style=social)](https://twitter.com/NeuroML) [![Gitter](https://badges.gitter.im/NeuroML/community.svg)](https://gitter.im/NeuroML/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) [![DOI](https://zenodo.org/badge/27832592.svg)](https://zenodo.org/doi/10.5281/zenodo.5744044) [![All Contributors](https://img.shields.io/badge/all_contributors-17-orange.svg?style=flat-square)](#contributors-) A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models. Builds on: [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) & [PyLEMS](https://github.com/LEMS/pylems) and wraps functionality from [jNeuroML](https://github.com/NeuroML/jNeuroML). Installation ------------ ### Dependencies pyNeuroML relies on additional software to carry out its functions: - Java Runtime environment (JRE) - dot (from [Graphviz](http://graphviz.org/)) - lxml On most Linux systems, these can be installed using the default package manager. On Ubuntu based distributions: sudo apt-get install python-lxml graphviz openjdk-11-jdk ### Pip pyNeuroML can be installed with pip (preferably in a [virtual environment](https://docs.python.org/3/tutorial/venv.html)): pip install pyneuroml A number of extra packages are also provided for convenience. You can install these to pull in other dependencies if required: pip install pyneuroml[neuron] # for NEURON simulation backend pip install pyneuroml[brian] # for Brian2 simulation backend pip install pyneuroml[netpyne] # for NetPyNE simulation backend pip install pyneuroml[povray] # for povray functions pip install pyneuroml[hdf5] # for HDF5 support pip install pyneuroml[analysis] # for analysis functions pip install pyneuroml[tune] # for tuning/fitting functions pip install pyneuroml[vispy] # for 3D interactive morphology plotting using vispy pip install pyneuroml[plotly] # for interactive plotting with plotly pip install pyneuroml[nsg] # pulls in pynsgr to use NSG pip install pyneuroml[combine] # includes libsbml, libsedml pip install pyneuroml[tellurium] # for Tellurium simulation backend pip install pyneuroml[all] # installs all of the above pip install pyneuroml[dev] # installs all of the above and other test related packages pip install pyneuroml[doc] # for building documentation Please see the `setup.cfg` file for more details. ### Fedora The [NeuroFedora](https://neuro.fedoraproject.org) community initiative provides pyNeuroML for use on the [Fedora Linux Distribution](https://getfedora.org). Fedora users can install pyNeuroML using the following commands: sudo dnf copr enable @neurofedora/neurofedora-extra sudo dnf install python3-pyneuroml This will also pull in all the necessary dependencies (Java, lxml, graphviz). Please see the [project documentation](https://docs.fedoraproject.org/en-US/neurofedora/copr/) for more information. ### Installation from the source Clone the repository: git clone https://github.com/NeuroML/pyNeuroML.git cd pyNeuroML It should be possible to install pyNeuroML using just: pip install . To develop pyNeuroML, you can use the `dev` extra and the `development` branch: git clone https://github.com/NeuroML/pyNeuroML.git cd pyNeuroML git checkout development pip install .[dev] Current/planned features ------------------------ **1) Single Python package for NeuroML2/LEMS** One Python package which can be installed using pip & a user has everything they need to work with NeuroML2/LEMS files: - libNeuroML - PyLEMS - A bundled version of jNeuroML which can be used to run simulations **2) Run models using jNeuroML or PyLEMS** Ability to run NeuroML2/LEMS models using jLEMS/jNeuroML (with [bundled jar](https://github.com/NeuroML/pyNeuroML/tree/master/pyneuroml/lib)) or PyLEMS (todo...) Uses similar command line interface to jNeuroML, i.e. based on jnml Try: pynml -h to list current options. **3) Access to export & import options of jNeuroML** All export & import options of jNeuroML available through easy command line interface (see [here](https://github.com/NeuroML/pyNeuroML/issues/21) for progress) & through Python methods. Example of export of NeuroML2/LEMS to NEURON and execution of generated code using single method is [here](https://github.com/NeuroML/pyNeuroML/blob/master/examples/run_jneuroml_plot_matplotlib.py#L21). **4) Helper Python scripts** Lots of helper scripts for commonly used functions, e.g. [generating a firing frequency vs injected current plot](https://github.com/NeuroML/pyNeuroML/blob/master/pyneuroml/analysis/__init__.py#L8), [generating a LEMS file for use with a NeuroML2 file](https://github.com/NeuroML/pyNeuroML/blob/master/pyneuroml/lems/__init__.py), **5) Analysis of ion channels** Generation of plots of activation rates for ion channels from NeuroML2 channel file ([example](https://github.com/NeuroML/pyNeuroML/blob/master/examples/analyseNaNml2.sh)): pynml-channelanalysis NaConductance.channel.nml Generation of plots of activation rates for ion channels from NEURON mod file ([example](https://github.com/NeuroML/pyNeuroML/blob/master/examples/analyseNaMod.sh)): pynml-modchananalysis NaConductance -modFile NaConductance.mod See [here](http://www.opensourcebrain.org/docs#Converting_To_NeuroML2) for more. **6) Home for existing functionality distributed in various places** Incorporate ChannelML2NeuroML2beta.xsl for updating ChannelML (coming soon...) **7) NEURON to NeuroML2** Scripts for converting NEURON to NeuroML2 - Export morphologies (plus channels, soon). See [here](https://github.com/NeuroML/pyNeuroML/blob/master/examples/export_neuroml2.py). - mod files - make best guess at initial NeuroML2 form (todo) **8) Export of images/movies from cell/networks** Files can be generated for [POV-Ray](http://www.povray.org/) which can be used to generate high resolution images and even sequences of images for creating movies. try: pynml-povray -h **9) Tuning cell models in NeuroML 2** Builds on [Neurotune](https://github.com/NeuralEnsemble/neurotune) and [pyelectro](https://github.com/NeuralEnsemble/pyelectro). See [here](https://github.com/NeuroML/pyNeuroML/blob/master/examples/tuneHHCell.py) for example. **9) Planned functionality** Built in viewer of cells in 3D? Mayavi? More closely tied to PyNN? ## Contributors
Padraig Gleeson
Padraig Gleeson
πŸ› πŸ’» πŸ–‹ πŸ”£ πŸ“– 🎨 πŸ“‹ πŸ€” πŸš‡ 🚧 πŸ§‘β€πŸ« πŸ“¦ πŸ“† πŸ’¬ πŸ”¬ πŸ‘€ πŸ”§ βœ… πŸ“’ πŸ““		 Ankur Sinha
Ankur Sinha
πŸ› πŸ’» πŸ–‹ πŸ”£ πŸ“– 🎨 πŸ“‹ πŸ€” πŸ§‘β€πŸ« πŸ“¦ πŸ’¬ πŸ”¬		 Boris Marin
Boris Marin
πŸ› πŸ’» πŸ–‹ πŸ”£ πŸ“– 🎨 πŸ“‹ πŸ€” πŸš‡ 🚧 πŸ“¦ πŸ’¬ πŸ”¬ πŸ‘€ πŸ”§ πŸ““		 Richard C Gerkin
Richard C Gerkin
πŸ› πŸ’» πŸ€” 🚧 πŸ“¦ πŸ”¬ πŸ‘€ πŸ”§ πŸ““		 David Lung
David Lung
πŸ› πŸ’» 🚧 πŸ”§ πŸ““		 Mark Watts
Mark Watts
πŸ› πŸ’»		 Chaitanya Chintaluri
Chaitanya Chintaluri
πŸ› πŸ’»
34383c
34383c
πŸ› πŸ’»		 Johannes Rieke
Johannes Rieke
πŸ› πŸ’»		 AndrΓ‘s Ecker
AndrΓ‘s Ecker
πŸ› πŸ’»		 Rokas Stanislovas
Rokas Stanislovas
πŸ› πŸ’»		 Robert Vickerstaff
Robert Vickerstaff
πŸ’» ⚠️		 Giannis Daras
Giannis Daras
πŸ› πŸ€” πŸ‘€ πŸ’»		 Dhruvanshu-Joshi
Dhruvanshu-Joshi
πŸ› πŸ€”
AdityaBITMESRA
AdityaBITMESRA
πŸ› πŸ€” πŸ’» πŸ‘€		 Y. Budhachandra
Y. Budhachandra
πŸ’» ⚠️		 Stella
Stella
πŸ’» πŸ€”
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