{ "info": { "author": "PyLEMS authors and contributors", "author_email": "gautham@lisphacker.org, 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": "PyLEMS \n======\n\nA LEMS (http://lems.github.io/LEMS) simulator written in Python which can be used \nto run NeuroML2 (http://neuroml.org/neuroml2.php) models.\n\nFor more about PyLEMS see:\n\nMichael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver and Padraig Gleeson,\n**libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience**\n[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00038/abstract), doi: 10.3389/fninf.2014.00038\n\n_**PLEASE CITE THE PAPER ABOVE IF YOU USE PYLEMS!**_\n\nFor more details on LEMS see: \n\nRobert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini and R. Angus Silver, \n**LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2**, \n[Frontiers in Neuroinformatics 2014](http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00079/abstract), doi: 10.3389/fninf.2014.00079\n\n\nInstallation\n------------\n\nA stable version of PyLEMS is [available on PyPI](https://pypi.python.org/pypi/PyLEMS) using [pip](https://pip.pypa.io/en/latest/installing.html):\n\n pip install pylems\n\nTo install as root:\n\n sudo pip install pylems\n\nAlternatively, you can obtain the latest version with\n\n git clone https://github.com/LEMS/pylems.git\n cd pylems \n git checkout development # optional\n sudo python setup.py install\n\nUsage as a LEMS model simulator\n-------------------------------\n\n pylems [options] LEMS_file\n\n**Options**\n\n- -I/-include path - Adds a directory to the model file include search path\n\n\nExamples\n--------\n\n**NeuroML examples (from https://github.com/NeuroML/NeuroML2/tree/development/NeuroML2CoreTypes)**\n\n- Example 0 -- Working\n- Example 1 -- Working\n- Example 2 -- Working\n- Example 3 -- Working\n- Example 4 -- Not working (Unsupported in PyLEMS: KSChannel)\n- Example 5 -- Working\n- Example 6 -- Working\n- Example 7 -- Working\n- Example 8 -- Working\n- Example 9 -- Working\n- Example 10 -- Working\n- Example 11 -- Working\n- Example 12 -- Not working (Unsupported in PyLEMS: Property)\n- Example 13 -- Working\n- Example 14 -- Not working (Unsupported in PyLEMS: Property)\n- Example 15 -- Working\n- Example 16 -- Working (apart from spikeArray)\n- Example 17 -- Working\n- Example 18 -- Working\n\n\n**LEMS examples (in directory examples)**\n\n- example1.xml -- Working\n- example2.xml -- Working\n- example3.xml -- Working\n- example4.xml -- Not working (Unsupported in PyLEMS: KSChannel)\n- example5.xml -- Not working (Unsupported in PyLEMS: KSChannel)\n- example6.xml -- Working\n-- TODO: Rest of examples 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