{ "info": { "author": "Padraig Gleeson", "author_email": "p.gleeson@gmail.com", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", "Natural Language :: English", "Operating System :: OS Independent", "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.2", "Topic :: Scientific/Engineering" ], "description": "pyNeuroML\n=========\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### Pip \n\npyNeuroML can be installed with pip:\n\n sudo pip install pyneuroml\n\nYou may need to install lxml on Linux with:\n\n sudo apt-get install python-lxml\n\n### Installation from 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 sudo pip install . -r requirements.txt\n \nYou **may** have to install lxml and the development version of [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) manually:\n\n apt-get install python-lxml\n cd ..\n git clone https://github.com/NeuralEnsemble/libNeuroML.git\n cd libNeuroML\n git checkout development\n sudo python setup.py install\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\t\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\t\n**9) Planned functionality**\n\nBuilt in viewer of cells in 3D? 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