From p.gleeson at ucl.ac.uk Fri Feb 15 11:45:52 2013 From: p.gleeson at ucl.ac.uk (Padraig Gleeson) Date: Fri, 15 Feb 2013 11:45:52 +0000 Subject: [neuroConstruct] Update on LEMS & NeuroML 2 developments Message-ID: <511E1FF0.4080108@ucl.ac.uk> Hi, We've been busy in a few different directions recently with developments for NeuroML 2 and LEMS so probably time for a quick update. LEMS - The main specifications for LEMS (Low Entropy Model Specification language) has been moved here: https://github.com/LEMS/LEMS. This currently consists of the XML Schema for LEMS, but the documentation, core examples etc. will be moved here also from the Java & Python repositories below. - jLEMS, or the Java reference implementation of LEMS by Robert Cannon has been moved here: https://github.com/LEMS/jLEMS. This includes a number of examples which can be read in & executed by jLEMS and has the most up to date documentation for LEMS elements (http://lems.github.com/jLEMS/elements.html). - PyLEMS (you guessed it, a Python implementation of LEMS) developed by Gautham Ganapathy is here: https://github.com/LEMS/pylems, and uses the same updated version of LEMS as jLEMS and can parse/validate/simulate most of the same examples. NeuroML 2 - The main repository for NeuroML 2 specifications is here: https://github.com/NeuroML/NeuroML2. This includes the Schemas, including the NeuroML 2 beta schema , and the LEMS ComponentTypes which define the structure and behaviour of elements of NeuroML 2. These definitions can be viewed online for a (hopefully) clearer view of their structure, e.g. izhikevichCell , nmdaSynapse , sineGenerator , etc. - A number of Java packages modules for handling NeuroML have been created here . One of these, org.neuroml.model , is a Java API for reading, writing & validating NeuroML 2. Others include packages for exporting NeuroML & LEMS models to various formats. These packages use Maven to make it easier to incorporate them into other Java applications. We plan to gather all these NeuroML/LEMS packages together into a single downloadable package with a simple command line interface for reading/writing/executing/converting models. - The Python API for NeuroML 2, libNeuroML , is undergoing major refactoring, but the existing version should still work fine for reading/writing NML2. Please get in contact with Mike Vella or myself if you're keen to use this. This initiative is closely linked to a Python API for multicompartmental modelling, Pyramidal , which will further increase interoperability between NeuroML & PyNN. Hope that provides a good overview of what's available at the moment. As suggested most of these initiatives are under active development, and offers of help or just feedback are more than welcome! These developments are also closely related to our work for the Open Source Brain repository (http://opensourcebrain.org). More exciting announcements about that coming soon! Regards, The NeuroML, LEMS & OSB teams ----------------------------------------------------- Padraig Gleeson Room 321, Anatomy Building Department of Neuroscience, Physiology& Pharmacology University College London Gower Street London WC1E 6BT United Kingdom +44 207 679 3214 p.gleeson at ucl.ac.uk ----------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: