[Comp-neuro] New release of NeuroML 2 and LEMS and two recent publications

Padraig Gleeson p.gleeson at ucl.ac.uk
Mon Oct 6 16:20:42 CEST 2014

Dear colleagues,

We are happy to announce a new stable release (version 2, beta 3) of the 
NeuroML language for model specification in computational neuroscience.


NeuroML allows specification of models of systems from integrate and 
fire cells up to complex 3D networks of multicompartmental neurons. 
NeuroML version 2 has been extensively redesigned to be built on a new 
language, LEMS, which allows machine readable definitions of model 
structure and dynamics. This facilitates model transparency, portability 
and code generation. LEMS and NeuroML 2 are described in detail in:

Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, 
Boris Marin, Eugenio Piasini and R. Angus Silver, *LEMS: A language for 
expressing complex biological models in concise and hierarchical form 
and its use in underpinning NeuroML 2*, Frontiers in Neuroinformatics 
2014, doi: 10.3389/fninf.2014.00079

There are libraries for reading, writing and simulating NeuroML models 
in Java (https://github.com/NeuroML/jNeuroML) and Python. The Python 
APIs for NeuroML and LEMS have recently been described in:

Michael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, 
Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver and Padraig 
Gleeson, *libNeuroML and PyLEMS: using Python to combine procedural and 
declarative modeling approaches in computational neuroscience*, 
Frontiers in Neuroinformatics 2014, doi: 10.3389/fninf.2014.00038

The growing number (30+) of tools, libraries and databases supporting 
NeuroML v1 and/or NeuroML v2 are listed here:


Open Source Brain is a repository of models in computational 
neuroscience which actively supports open, collaborative development of 
models, as well as conversion to simulator independent formats including 
NeuroML (over 500 valid NeuroML 2 cells/channels/synapses on OSB at last 
count). An overview of the models currently present and the 
formats/simulators supported can be found here:


The NeuroML development community

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

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