pyNeuroML
=========
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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
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<table>
<tbody>
<tr>
<td align="center" valign="top" width="14.28%"><a href="http://www.opensourcebrain.org/"><img src="https://avatars.githubusercontent.com/u/1556687?v=4?s=100" width="100px;" alt="Padraig Gleeson"/><br /><sub><b>Padraig Gleeson</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Apgleeson" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=pgleeson" title="Code">💻</a> <a href="#content-pgleeson" title="Content">🖋</a> <a href="#data-pgleeson" title="Data">🔣</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=pgleeson" title="Documentation">📖</a> <a href="#design-pgleeson" title="Design">🎨</a> <a href="#eventOrganizing-pgleeson" title="Event Organizing">📋</a> <a href="#ideas-pgleeson" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-pgleeson" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-pgleeson" title="Maintenance">🚧</a> <a href="#mentoring-pgleeson" title="Mentoring">🧑🏫</a> <a href="#platform-pgleeson" title="Packaging/porting to new platform">📦</a> <a href="#projectManagement-pgleeson" title="Project Management">📆</a> <a href="#question-pgleeson" title="Answering Questions">💬</a> <a href="#research-pgleeson" title="Research">🔬</a> <a href="https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3Apgleeson" title="Reviewed Pull Requests">👀</a> <a href="#tool-pgleeson" title="Tools">🔧</a> <a href="#tutorial-pgleeson" title="Tutorials">✅</a> <a href="#talk-pgleeson" title="Talks">📢</a> <a href="#userTesting-pgleeson" title="User Testing">📓</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://ankursinha.in/"><img src="https://avatars.githubusercontent.com/u/102575?v=4?s=100" width="100px;" alt="Ankur Sinha"/><br /><sub><b>Ankur Sinha</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Asanjayankur31" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=sanjayankur31" title="Code">💻</a> <a href="#content-sanjayankur31" title="Content">🖋</a> <a href="#data-sanjayankur31" title="Data">🔣</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=sanjayankur31" title="Documentation">📖</a> <a href="#design-sanjayankur31" title="Design">🎨</a> <a href="#eventOrganizing-sanjayankur31" title="Event Organizing">📋</a> <a href="#ideas-sanjayankur31" title="Ideas, Planning, & Feedback">🤔</a> <a href="#mentoring-sanjayankur31" title="Mentoring">🧑🏫</a> <a href="#platform-sanjayankur31" title="Packaging/porting to new platform">📦</a> <a href="#question-sanjayankur31" title="Answering Questions">💬</a> <a href="#research-sanjayankur31" title="Research">🔬</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/borismarin"><img src="https://avatars.githubusercontent.com/u/3452783?v=4?s=100" width="100px;" alt="Boris Marin"/><br /><sub><b>Boris Marin</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Aborismarin" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=borismarin" title="Code">💻</a> <a href="#content-borismarin" title="Content">🖋</a> <a href="#data-borismarin" title="Data">🔣</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=borismarin" title="Documentation">📖</a> <a href="#design-borismarin" title="Design">🎨</a> <a href="#eventOrganizing-borismarin" title="Event Organizing">📋</a> <a href="#ideas-borismarin" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-borismarin" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-borismarin" title="Maintenance">🚧</a> <a href="#platform-borismarin" title="Packaging/porting to new platform">📦</a> <a href="#question-borismarin" title="Answering Questions">💬</a> <a href="#research-borismarin" title="Research">🔬</a> <a href="https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3Aborismarin" title="Reviewed Pull Requests">👀</a> <a href="#tool-borismarin" title="Tools">🔧</a> <a href="#userTesting-borismarin" title="User Testing">📓</a></td>
<td align="center" valign="top" width="14.28%"><a href="http://rick.gerk.in/"><img src="https://avatars.githubusercontent.com/u/549787?v=4?s=100" width="100px;" alt="Richard C Gerkin"/><br /><sub><b>Richard C Gerkin</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Argerkin" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=rgerkin" title="Code">💻</a> <a href="#ideas-rgerkin" title="Ideas, Planning, & Feedback">🤔</a> <a href="#maintenance-rgerkin" title="Maintenance">🚧</a> <a href="#platform-rgerkin" title="Packaging/porting to new platform">📦</a> <a href="#research-rgerkin" title="Research">🔬</a> <a href="https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3Argerkin" title="Reviewed Pull Requests">👀</a> <a href="#tool-rgerkin" title="Tools">🔧</a> <a href="#userTesting-rgerkin" title="User Testing">📓</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/lungd"><img src="https://avatars.githubusercontent.com/u/5890526?v=4?s=100" width="100px;" alt="David Lung"/><br /><sub><b>David Lung</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Alungd" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=lungd" title="Code">💻</a> <a href="#maintenance-lungd" title="Maintenance">🚧</a> <a href="#tool-lungd" title="Tools">🔧</a> <a href="#userTesting-lungd" title="User Testing">📓</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://www.thispersondoesnotexist.com/"><img src="https://avatars.githubusercontent.com/u/1487560?v=4?s=100" width="100px;" alt="Mark Watts"/><br /><sub><b>Mark Watts</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Amwatts15" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=mwatts15" title="Code">💻</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://chchaitanya.wordpress.com/"><img src="https://avatars.githubusercontent.com/u/546703?v=4?s=100" width="100px;" alt="Chaitanya Chintaluri "/><br /><sub><b>Chaitanya Chintaluri </b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Accluri" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=ccluri" title="Code">💻</a></td>
</tr>
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<td align="center" valign="top" width="14.28%"><a href="https://github.com/34383c"><img src="https://avatars.githubusercontent.com/u/17238193?v=4?s=100" width="100px;" alt="34383c"/><br /><sub><b>34383c</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3A34383c" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=34383c" title="Code">💻</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/jrieke"><img src="https://avatars.githubusercontent.com/u/5103165?v=4?s=100" width="100px;" alt="Johannes Rieke"/><br /><sub><b>Johannes Rieke</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Ajrieke" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=jrieke" title="Code">💻</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/andrisecker"><img src="https://avatars.githubusercontent.com/u/13274870?v=4?s=100" width="100px;" alt="András Ecker"/><br /><sub><b>András Ecker</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Aandrisecker" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=andrisecker" title="Code">💻</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/RokasSt"><img src="https://avatars.githubusercontent.com/u/12904422?v=4?s=100" width="100px;" alt="Rokas Stanislovas"/><br /><sub><b>Rokas Stanislovas</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3ARokasSt" title="Bug reports">🐛</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=RokasSt" title="Code">💻</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/robertvi"><img src="https://avatars.githubusercontent.com/u/456100?v=4?s=100" width="100px;" alt="Robert Vickerstaff"/><br /><sub><b>Robert Vickerstaff</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/commits?author=robertvi" title="Code">💻</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=robertvi" title="Tests">⚠️</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/lej0hn"><img src="https://avatars.githubusercontent.com/u/72049569?v=4?s=100" width="100px;" alt="Giannis Daras"/><br /><sub><b>Giannis Daras</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3Alej0hn" title="Bug reports">🐛</a> <a href="#ideas-lej0hn" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3Alej0hn" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=lej0hn" title="Code">💻</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/Dhruvanshu-Joshi"><img src="https://avatars.githubusercontent.com/u/104030847?v=4?s=100" width="100px;" alt="Dhruvanshu-Joshi"/><br /><sub><b>Dhruvanshu-Joshi</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3ADhruvanshu-Joshi" title="Bug reports">🐛</a> <a href="#ideas-Dhruvanshu-Joshi" title="Ideas, Planning, & Feedback">🤔</a></td>
</tr>
<tr>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/AdityaBITMESRA"><img src="https://avatars.githubusercontent.com/u/147182147?v=4?s=100" width="100px;" alt="AdityaBITMESRA"/><br /><sub><b>AdityaBITMESRA</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/issues?q=author%3AAdityaBITMESRA" title="Bug reports">🐛</a> <a href="#ideas-AdityaBITMESRA" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=AdityaBITMESRA" title="Code">💻</a> <a href="https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3AAdityaBITMESRA" title="Reviewed Pull Requests">👀</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/YBCS"><img src="https://avatars.githubusercontent.com/u/29734619?v=4?s=100" width="100px;" alt="Y. Budhachandra"/><br /><sub><b>Y. Budhachandra</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/commits?author=YBCS" title="Code">💻</a> <a href="https://github.com/NeuroML/pyNeuroML/commits?author=YBCS" title="Tests">⚠️</a></td>
<td align="center" valign="top" width="14.28%"><a href="https://github.com/stellaprins"><img src="https://avatars.githubusercontent.com/u/30465823?v=4?s=100" width="100px;" alt="Stella"/><br /><sub><b>Stella</b></sub></a><br /><a href="https://github.com/NeuroML/pyNeuroML/commits?author=stellaprins" title="Code">💻</a> <a href="#ideas-stellaprins" title="Ideas, Planning, & Feedback">🤔</a></td>
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"description": "pyNeuroML\n=========\n\n[](https://github.com/NeuroML/pyNeuroML/actions/workflows/ci.yml)\n[](https://pypi.org/project/pyNeuroML/)\n[](https://pypi.org/project/pyNeuroML/)\n[](https://github.com/NeuroML/pyNeuroML/blob/master/LICENSE.lesser)\n[](https://github.com/NeuroML/pyNeuroML/pulls)\n[](https://github.com/NeuroML/pyNeuroML/issues)\n[](https://pyneuroml.readthedocs.io/en/latest/?badge=latest)\n[](https://github.com/NeuroML)\n[](https://twitter.com/NeuroML)\n[](https://gitter.im/NeuroML/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)\n<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->\n[](#contributors-)\n<!-- ALL-CONTRIBUTORS-BADGE:END -->\n\nA single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.\n\nBuilds on: [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) & [PyLEMS](https://github.com/LEMS/pylems) and wraps functionality from [jNeuroML](https://github.com/NeuroML/jNeuroML).\n\nInstallation\n------------\n\n### Dependencies\n\npyNeuroML relies on additional software to carry out its functions:\n\n- Java Runtime environment (JRE)\n- dot (from [Graphviz](http://graphviz.org/))\n- lxml\n\nOn most Linux systems, these can be installed using the default package manager.\nOn Ubuntu based distributions:\n\n sudo apt-get install python-lxml graphviz openjdk-11-jdk\n\n\n### Pip\n\npyNeuroML can be installed with pip (preferably in a [virtual environment](https://docs.python.org/3/tutorial/venv.html)):\n\n pip install pyneuroml\n\n\nA number of extra packages are also provided for convenience. You can install these to pull in other dependencies if required:\n\n\n pip install pyneuroml[neuron] # for NEURON simulation backend\n pip install pyneuroml[brian] # for Brian2 simulation backend\n pip install pyneuroml[netpyne] # for NetPyNE simulation backend\n pip install pyneuroml[povray] # for povray functions\n pip install pyneuroml[hdf5] # for HDF5 support\n pip install pyneuroml[analysis] # for analysis functions\n pip install pyneuroml[tune] # for tuning/fitting functions\n pip install pyneuroml[vispy] # for 3D interactive morphology plotting using vispy\n pip install pyneuroml[plotly] # for interactive plotting with plotly\n pip install pyneuroml[nsg] # pulls in pynsgr to use NSG\n pip install pyneuroml[combine] # includes libsbml, libsedml\n pip install pyneuroml[tellurium] # for Tellurium simulation backend\n pip install pyneuroml[all] # installs all of the above\n pip install pyneuroml[dev] # installs all of the above and other test related packages\n pip install pyneuroml[doc] # for building documentation\n\n\nPlease see the `setup.cfg` file for more details.\n\n\n### Fedora\n\nThe [NeuroFedora](https://neuro.fedoraproject.org) community initiative provides pyNeuroML for use on the [Fedora Linux Distribution](https://getfedora.org).\nFedora users can install pyNeuroML using the following commands:\n\n sudo dnf copr enable @neurofedora/neurofedora-extra\n sudo dnf install python3-pyneuroml\n\nThis will also pull in all the necessary dependencies (Java, lxml, graphviz).\nPlease see the [project documentation](https://docs.fedoraproject.org/en-US/neurofedora/copr/) for more information.\n\n### Installation from the source\n\nClone the repository:\n\n git clone https://github.com/NeuroML/pyNeuroML.git\n cd pyNeuroML\n\nIt should be possible to install pyNeuroML using just:\n\n pip install .\n\nTo develop pyNeuroML, you can use the `dev` extra and the `development` branch:\n\n git clone https://github.com/NeuroML/pyNeuroML.git\n cd pyNeuroML\n git checkout development\n pip install .[dev]\n\n\nCurrent/planned features\n------------------------\n\n**1) Single Python package for NeuroML2/LEMS**\n\nOne Python package which can be installed using pip & a user has everything they need to work with NeuroML2/LEMS files:\n\n- libNeuroML\n- PyLEMS\n- A bundled version of jNeuroML which can be used to run simulations\n\n**2) Run models using jNeuroML or PyLEMS**\n\nAbility to run NeuroML2/LEMS models using jLEMS/jNeuroML (with [bundled jar](https://github.com/NeuroML/pyNeuroML/tree/master/pyneuroml/lib)) or PyLEMS (todo...)\n\nUses similar command line interface to jNeuroML, i.e. based on jnml\n\nTry:\n\n pynml -h\n\nto list current options.\n\n\n**3) Access to export & import options of jNeuroML**\n\nAll 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.\n\nExample 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).\n\n**4) Helper Python scripts**\n\nLots 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),\n\n**5) Analysis of ion channels**\n\nGeneration of plots of activation rates for ion channels from NeuroML2 channel file ([example](https://github.com/NeuroML/pyNeuroML/blob/master/examples/analyseNaNml2.sh)):\n\n pynml-channelanalysis NaConductance.channel.nml\n\nGeneration of plots of activation rates for ion channels from NEURON mod file ([example](https://github.com/NeuroML/pyNeuroML/blob/master/examples/analyseNaMod.sh)):\n\n pynml-modchananalysis NaConductance -modFile NaConductance.mod\n\nSee [here](http://www.opensourcebrain.org/docs#Converting_To_NeuroML2) for more.\n\n**6) Home for existing functionality distributed in various places**\n\nIncorporate ChannelML2NeuroML2beta.xsl for updating ChannelML (coming soon...)\n\n**7) NEURON to NeuroML2**\n\nScripts for converting NEURON to NeuroML2\n\n- Export morphologies (plus channels, soon). See [here](https://github.com/NeuroML/pyNeuroML/blob/master/examples/export_neuroml2.py).\n\n- mod files - make best guess at initial NeuroML2 form (todo)\n\n**8) Export of images/movies from cell/networks**\n\nFiles 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:\n\n pynml-povray -h\n\n**9) Tuning cell models in NeuroML 2**\n\nBuilds 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.\n\n**9) Planned functionality**\n\nBuilt in viewer of cells in 3D? Mayavi?\nMore closely tied to PyNN?\n\n\n## Contributors\n\n<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->\n<!-- prettier-ignore-start -->\n<!-- markdownlint-disable -->\n<table>\n <tbody>\n <tr>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"http://www.opensourcebrain.org/\"><img src=\"https://avatars.githubusercontent.com/u/1556687?v=4?s=100\" width=\"100px;\" alt=\"Padraig Gleeson\"/><br /><sub><b>Padraig Gleeson</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3Apgleeson\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=pgleeson\" title=\"Code\">\ud83d\udcbb</a> <a href=\"#content-pgleeson\" title=\"Content\">\ud83d\udd8b</a> <a href=\"#data-pgleeson\" title=\"Data\">\ud83d\udd23</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=pgleeson\" title=\"Documentation\">\ud83d\udcd6</a> <a href=\"#design-pgleeson\" title=\"Design\">\ud83c\udfa8</a> <a href=\"#eventOrganizing-pgleeson\" title=\"Event Organizing\">\ud83d\udccb</a> <a href=\"#ideas-pgleeson\" title=\"Ideas, Planning, & Feedback\">\ud83e\udd14</a> <a href=\"#infra-pgleeson\" title=\"Infrastructure (Hosting, Build-Tools, etc)\">\ud83d\ude87</a> <a href=\"#maintenance-pgleeson\" title=\"Maintenance\">\ud83d\udea7</a> <a href=\"#mentoring-pgleeson\" title=\"Mentoring\">\ud83e\uddd1\u200d\ud83c\udfeb</a> <a href=\"#platform-pgleeson\" title=\"Packaging/porting to new platform\">\ud83d\udce6</a> <a href=\"#projectManagement-pgleeson\" title=\"Project Management\">\ud83d\udcc6</a> <a href=\"#question-pgleeson\" title=\"Answering Questions\">\ud83d\udcac</a> <a href=\"#research-pgleeson\" title=\"Research\">\ud83d\udd2c</a> <a href=\"https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3Apgleeson\" title=\"Reviewed Pull Requests\">\ud83d\udc40</a> <a href=\"#tool-pgleeson\" title=\"Tools\">\ud83d\udd27</a> <a href=\"#tutorial-pgleeson\" title=\"Tutorials\">\u2705</a> <a href=\"#talk-pgleeson\" title=\"Talks\">\ud83d\udce2</a> <a href=\"#userTesting-pgleeson\" title=\"User Testing\">\ud83d\udcd3</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://ankursinha.in/\"><img src=\"https://avatars.githubusercontent.com/u/102575?v=4?s=100\" width=\"100px;\" alt=\"Ankur Sinha\"/><br /><sub><b>Ankur Sinha</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3Asanjayankur31\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=sanjayankur31\" title=\"Code\">\ud83d\udcbb</a> <a href=\"#content-sanjayankur31\" title=\"Content\">\ud83d\udd8b</a> <a href=\"#data-sanjayankur31\" title=\"Data\">\ud83d\udd23</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=sanjayankur31\" title=\"Documentation\">\ud83d\udcd6</a> <a href=\"#design-sanjayankur31\" title=\"Design\">\ud83c\udfa8</a> <a href=\"#eventOrganizing-sanjayankur31\" title=\"Event Organizing\">\ud83d\udccb</a> <a href=\"#ideas-sanjayankur31\" title=\"Ideas, Planning, & Feedback\">\ud83e\udd14</a> <a href=\"#mentoring-sanjayankur31\" title=\"Mentoring\">\ud83e\uddd1\u200d\ud83c\udfeb</a> <a href=\"#platform-sanjayankur31\" title=\"Packaging/porting to new platform\">\ud83d\udce6</a> <a href=\"#question-sanjayankur31\" title=\"Answering Questions\">\ud83d\udcac</a> <a href=\"#research-sanjayankur31\" title=\"Research\">\ud83d\udd2c</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/borismarin\"><img src=\"https://avatars.githubusercontent.com/u/3452783?v=4?s=100\" width=\"100px;\" alt=\"Boris Marin\"/><br /><sub><b>Boris Marin</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3Aborismarin\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=borismarin\" title=\"Code\">\ud83d\udcbb</a> <a href=\"#content-borismarin\" title=\"Content\">\ud83d\udd8b</a> <a href=\"#data-borismarin\" title=\"Data\">\ud83d\udd23</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=borismarin\" title=\"Documentation\">\ud83d\udcd6</a> <a href=\"#design-borismarin\" title=\"Design\">\ud83c\udfa8</a> <a href=\"#eventOrganizing-borismarin\" title=\"Event Organizing\">\ud83d\udccb</a> <a href=\"#ideas-borismarin\" title=\"Ideas, Planning, & Feedback\">\ud83e\udd14</a> <a href=\"#infra-borismarin\" title=\"Infrastructure (Hosting, Build-Tools, etc)\">\ud83d\ude87</a> <a href=\"#maintenance-borismarin\" title=\"Maintenance\">\ud83d\udea7</a> <a href=\"#platform-borismarin\" title=\"Packaging/porting to new platform\">\ud83d\udce6</a> <a href=\"#question-borismarin\" title=\"Answering Questions\">\ud83d\udcac</a> <a href=\"#research-borismarin\" title=\"Research\">\ud83d\udd2c</a> <a href=\"https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3Aborismarin\" title=\"Reviewed Pull Requests\">\ud83d\udc40</a> <a href=\"#tool-borismarin\" title=\"Tools\">\ud83d\udd27</a> <a href=\"#userTesting-borismarin\" title=\"User Testing\">\ud83d\udcd3</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"http://rick.gerk.in/\"><img src=\"https://avatars.githubusercontent.com/u/549787?v=4?s=100\" width=\"100px;\" alt=\"Richard C Gerkin\"/><br /><sub><b>Richard C Gerkin</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3Argerkin\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=rgerkin\" title=\"Code\">\ud83d\udcbb</a> <a href=\"#ideas-rgerkin\" title=\"Ideas, Planning, & Feedback\">\ud83e\udd14</a> <a href=\"#maintenance-rgerkin\" title=\"Maintenance\">\ud83d\udea7</a> <a href=\"#platform-rgerkin\" title=\"Packaging/porting to new platform\">\ud83d\udce6</a> <a href=\"#research-rgerkin\" title=\"Research\">\ud83d\udd2c</a> <a href=\"https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3Argerkin\" title=\"Reviewed Pull Requests\">\ud83d\udc40</a> <a href=\"#tool-rgerkin\" title=\"Tools\">\ud83d\udd27</a> <a href=\"#userTesting-rgerkin\" title=\"User Testing\">\ud83d\udcd3</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/lungd\"><img src=\"https://avatars.githubusercontent.com/u/5890526?v=4?s=100\" width=\"100px;\" alt=\"David Lung\"/><br /><sub><b>David Lung</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3Alungd\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=lungd\" title=\"Code\">\ud83d\udcbb</a> <a href=\"#maintenance-lungd\" title=\"Maintenance\">\ud83d\udea7</a> <a href=\"#tool-lungd\" title=\"Tools\">\ud83d\udd27</a> <a href=\"#userTesting-lungd\" title=\"User Testing\">\ud83d\udcd3</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://www.thispersondoesnotexist.com/\"><img src=\"https://avatars.githubusercontent.com/u/1487560?v=4?s=100\" width=\"100px;\" alt=\"Mark Watts\"/><br /><sub><b>Mark Watts</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3Amwatts15\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=mwatts15\" title=\"Code\">\ud83d\udcbb</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://chchaitanya.wordpress.com/\"><img src=\"https://avatars.githubusercontent.com/u/546703?v=4?s=100\" width=\"100px;\" alt=\"Chaitanya Chintaluri \"/><br /><sub><b>Chaitanya Chintaluri </b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3Accluri\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=ccluri\" title=\"Code\">\ud83d\udcbb</a></td>\n </tr>\n <tr>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/34383c\"><img src=\"https://avatars.githubusercontent.com/u/17238193?v=4?s=100\" width=\"100px;\" alt=\"34383c\"/><br /><sub><b>34383c</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3A34383c\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=34383c\" title=\"Code\">\ud83d\udcbb</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/jrieke\"><img src=\"https://avatars.githubusercontent.com/u/5103165?v=4?s=100\" width=\"100px;\" alt=\"Johannes Rieke\"/><br /><sub><b>Johannes Rieke</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3Ajrieke\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=jrieke\" title=\"Code\">\ud83d\udcbb</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/andrisecker\"><img src=\"https://avatars.githubusercontent.com/u/13274870?v=4?s=100\" width=\"100px;\" alt=\"Andr\u00e1s Ecker\"/><br /><sub><b>Andr\u00e1s Ecker</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3Aandrisecker\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=andrisecker\" title=\"Code\">\ud83d\udcbb</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/RokasSt\"><img src=\"https://avatars.githubusercontent.com/u/12904422?v=4?s=100\" width=\"100px;\" alt=\"Rokas Stanislovas\"/><br /><sub><b>Rokas Stanislovas</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3ARokasSt\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=RokasSt\" title=\"Code\">\ud83d\udcbb</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/robertvi\"><img src=\"https://avatars.githubusercontent.com/u/456100?v=4?s=100\" width=\"100px;\" alt=\"Robert Vickerstaff\"/><br /><sub><b>Robert Vickerstaff</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=robertvi\" title=\"Code\">\ud83d\udcbb</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=robertvi\" title=\"Tests\">\u26a0\ufe0f</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/lej0hn\"><img src=\"https://avatars.githubusercontent.com/u/72049569?v=4?s=100\" width=\"100px;\" alt=\"Giannis Daras\"/><br /><sub><b>Giannis Daras</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3Alej0hn\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"#ideas-lej0hn\" title=\"Ideas, Planning, & Feedback\">\ud83e\udd14</a> <a href=\"https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3Alej0hn\" title=\"Reviewed Pull Requests\">\ud83d\udc40</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=lej0hn\" title=\"Code\">\ud83d\udcbb</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/Dhruvanshu-Joshi\"><img src=\"https://avatars.githubusercontent.com/u/104030847?v=4?s=100\" width=\"100px;\" alt=\"Dhruvanshu-Joshi\"/><br /><sub><b>Dhruvanshu-Joshi</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3ADhruvanshu-Joshi\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"#ideas-Dhruvanshu-Joshi\" title=\"Ideas, Planning, & Feedback\">\ud83e\udd14</a></td>\n </tr>\n <tr>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/AdityaBITMESRA\"><img src=\"https://avatars.githubusercontent.com/u/147182147?v=4?s=100\" width=\"100px;\" alt=\"AdityaBITMESRA\"/><br /><sub><b>AdityaBITMESRA</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/issues?q=author%3AAdityaBITMESRA\" title=\"Bug reports\">\ud83d\udc1b</a> <a href=\"#ideas-AdityaBITMESRA\" title=\"Ideas, Planning, & Feedback\">\ud83e\udd14</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=AdityaBITMESRA\" title=\"Code\">\ud83d\udcbb</a> <a href=\"https://github.com/NeuroML/pyNeuroML/pulls?q=is%3Apr+reviewed-by%3AAdityaBITMESRA\" title=\"Reviewed Pull Requests\">\ud83d\udc40</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/YBCS\"><img src=\"https://avatars.githubusercontent.com/u/29734619?v=4?s=100\" width=\"100px;\" alt=\"Y. Budhachandra\"/><br /><sub><b>Y. Budhachandra</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=YBCS\" title=\"Code\">\ud83d\udcbb</a> <a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=YBCS\" title=\"Tests\">\u26a0\ufe0f</a></td>\n <td align=\"center\" valign=\"top\" width=\"14.28%\"><a href=\"https://github.com/stellaprins\"><img src=\"https://avatars.githubusercontent.com/u/30465823?v=4?s=100\" width=\"100px;\" alt=\"Stella\"/><br /><sub><b>Stella</b></sub></a><br /><a href=\"https://github.com/NeuroML/pyNeuroML/commits?author=stellaprins\" title=\"Code\">\ud83d\udcbb</a> <a href=\"#ideas-stellaprins\" title=\"Ideas, Planning, & Feedback\">\ud83e\udd14</a></td>\n </tr>\n </tbody>\n <tfoot>\n <tr>\n <td align=\"center\" size=\"13px\" colspan=\"7\">\n <img src=\"https://raw.githubusercontent.com/all-contributors/all-contributors-cli/1b8533af435da9854653492b1327a23a4dbd0a10/assets/logo-small.svg\">\n <a href=\"https://all-contributors.js.org/docs/en/bot/usage\">Add your contributions</a>\n </img>\n </td>\n </tr>\n </tfoot>\n</table>\n\n<!-- markdownlint-restore -->\n<!-- prettier-ignore-end -->\n\n<!-- ALL-CONTRIBUTORS-LIST:END -->\n",
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