[Neuroinfo] 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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