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Towards NeuroML: Model Description Methods for Collaborative Modelling in Neuroscience

Goddard, Nigel H. and Hucka, Michael and Howell, Fred and Cornelis, Hugo and Shankar, Kavita and Beeman, David (2001) Towards NeuroML: Model Description Methods for Collaborative Modelling in Neuroscience. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 356 (1412). pp. 1209-1228. ISSN 0962-8436. PMCID PMC1088511. https://resolver.caltech.edu/CaltechAUTHORS:20121220-181928125

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Abstract

Biological nervous systems and the mechanisms underlying their operation exhibit astonishing complexity. Computational models of these systems have been correspondingly complex. As these models become ever more sophisticated, they become increasingly difficult to define, comprehend, manage and communicate. Consequently, for scientific understanding of biological nervous systems to progress, it is crucial for modellers to have software tools that support discussion, development and exchange of computational models. We describe methodologies that focus on these tasks, improving the ability of neuroscientists to engage in the modelling process. We report our findings on the requirements for these tools and discuss the use of declarative forms of model description—equivalent to object–oriented classes and database schema—which we call templates. We introduce NeuroML, a mark–up language for the neurosciences which is defined syntactically using templates, and its specific component intended as a common format for communication between modelling–related tools. Finally, we propose a template hierarchy for this modelling component of NeuroML, sufficient for describing models ranging in structural levels from neuron cell membranes to neural networks. These templates support both a framework for user–level interaction with models, and a high–performance framework for efficient simulation of the models.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1098/rstb.2001.0910DOIArticle
http://rstb.royalsocietypublishing.org/content/356/1412/1209PublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088511/PubMed CentralArticle
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Contact Email Address:nigel.goddard@ed.ac.uk
Additional Information:© 2001 The Royal Society. Published online August 29, 2001. We thank Dan Gardner, Robert Cannon,Marc-Oliver Gewaltig, Greg Hood, Paul Rogister, Michael Hines, Gully Burns and Henry Thompson for helpful discussions about the structure of NeuroML and this paper. This work was supported by National Institutes of Health Human Brain Project grants MH57358 and NF00002, and an Academic Equipment Grant (EDUD-7824- 000127-US) from Sun Microsystems, Inc., 901 San Antonio Road, Palo Alto, CA 94303.
Funders:
Funding AgencyGrant Number
NIHMH57358
NIHNF00002
Sun Microsystems, Inc.EDUD-7824-000127-US
Subject Keywords: NeuroML computational models simulation databases interoperability
Issue or Number:1412
PubMed Central ID:PMC1088511
Record Number:CaltechAUTHORS:20121220-181928125
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20121220-181928125
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:36089
Collection:CaltechAUTHORS
Deposited By: Linda Taddeo
Deposited On:21 Dec 2012 15:47
Last Modified:03 Oct 2019 04:34

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