[Comp-neuro] NeuroML: a simulator-independent language for describing biologically detailed neuronal and network models

Padraig Gleeson p.gleeson at ucl.ac.uk
Mon Jan 19 20:12:59 CET 2009


Dear all,

The NeuroML initiative web site has recently been revamped 
(http://www.neuroml.org), and a new version of the specifications has 
been released (v1.8.0).

NeuroML is a model description language which allows specification of 
components of biologically detailed neuronal models at many levels (e.g. 
ion channels, synaptic mechanisms, cells, networks). Examples of NeuroML 
files specifying each of these are available on the website. There are 
currently mappings available for most of these elements to the NEURON 
(http://www.neuron.yale.edu/neuron) and GENESIS 
(http://www.genesis-sim.org/GENESIS) simulators (and others are being 
added, e.g. to PSICS (http://www.psics.org)). The latest version of 
NEURON also natively supports import and export of cells in NeuroML 
format. neuroConstruct (http://www.neuroConstruct.org) is an application 
which facilitates the generation of simulation scripts for a number of 
simulators from models specified in NeuroML. The focus of the language 
is on multicompartmental conductance based neurons, but some simpler 
representations of neuronal models (e.g. basic I&F) are supported. The 
declarative model specifications of NeuroML are complementary to the 
procedural modelling language approach of PyNN 
(http://neuralensemble.org/trac/PyNN), and work is ongoing to ensure 
compatibility of these initiatives.

The ultimate success of NeuroML depends on a strong involvement of the 
user and developer community. Because the NeuroML language is being 
developed as an Open Source project 
(http://sourceforge.net/projects/neuroml) it is easy to contribute. We 
encourage those interested to play a part in the further development and 
improvement of the language. This can be done in two ways:
- by joining the mailing list at 
https://sourceforge.net/mail/?group_id=136437). Currently, requirements 
are being gathered for future versions of NeuroML 
(www.neuroml.org/NeuroMLValidator/ReqVersion2.jsp).
- by participating in a workshop (supported by the Wellcome Trust, NSF 
and INCF) in London on March 9-10th to further develop standards for 
describing models of channel kinetics and the biophysical properties of 
cells. Meeting attendees have already been invited, but please contact 
us if you feel your expertise would be particularly helpful for the 
workshop.

Padraig Gleeson
Sharon Crook
Angus Silver


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