[Comp-neuro] Publication on NeuroML, a model description language for computational neuroscience

pgleeson p.gleeson at ucl.ac.uk
Wed Jun 23 13:47:34 CEST 2010


Dear all,

A description of NeuroML (http://www.neuroml.org) has recently been
published in PLoS Computational Biology:

*NeuroML: A Language for Describing Data Driven Models of Neurons and
Networks with a High Degree of Biological Detail*
Padraig Gleeson, Sharon Crook, Robert C. Cannon, Michael L. Hines, Guy
O. Billings, Matteo Farinella, Thomas M. Morse, Andrew P. Davison,
Subhasis Ray, Upinder S. Bhalla, Simon R. Barnes, Yoana D. Dimitrova, R.
Angus Silver

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000815

NeuroML is an XML-based language for describing anatomically and
physiologically detailed cell and network models. It has multiple levels
that define cell morphologies, ion channel kinetics, synaptic
transmission (electrical and chemical) together with 3D network
structure and connectivity. These features allow many of the existing
conductance based neuron and network models to be defined in a simulator
independent form. Complete models or model components defined in NeuroML
can be mapped to a number of commonly used simulators. An increasing
number of open source tools for computational neuroscience support the
NeuroML language, see http://www.neuroml.org/tool_support.php.

The paper describes in detail the structure of version 1.8 (Levels 1-3,
MorphML, ChannelML, NetworkML), includes a detailed discussion of the
elements present at each level (see supporting text:
http://www.ploscompbiol.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pcbi.1000815.s001)
describes examples of NeuroML code, outlines current simulator support,
and validates NeuroML based models by comparing the behaviour of a
number of existing single cell and network models across simulators.
These models are also included with the latest version of neuroConstruct
(http://www.neuroconstruct.org), which can be used to generate scripts
for NEURON, GENESIS, MOOSE, PSICS and PyNN compliant simulators.

The NeuroML initiative is actively seeking input for version 2.0 of
NeuroML, which will incorporate greater interaction with complex
signalling pathways (via interactions with model elements in Systems
Biology languages such as SBML and CellML) and more complex compact
representations of network structures (in collaboration with the INCF
Program on Multiscale Modelling). To find out more, please see the
recent meeting minutes (News & Events on the homepage) and join the
mailing list
(https://lists.sourceforge.net/lists/listinfo/neuroml-technology) to be
kept up to date on developments.

Regards,

The NeuroML Team
Padraig Gleeson,
Sharon Crook,
Robert Cannon,
Angus Silver



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