[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.

http://www.neuroml.org/getneuroml

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:

http://www.neuroml.org/tool_support

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:

http://www.opensourcebrain.org/status

Regards,
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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