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NSDF: Neuroscience Simulation Data Format

Data interchange is emerging as an essential aspect of modern neuroscience. In the areas of computational neuroscience and systems biology there are multiple model definition formats, which have contributed strongly to the development of an ecosystem of simulation and analysis tools. Here we report...

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Detalles Bibliográficos
Autores principales: Ray, Subhasis, Chintaluri, Chaitanya, Bhalla, Upinder S., Wójcik, Daniel K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823348/
https://www.ncbi.nlm.nih.gov/pubmed/26585711
http://dx.doi.org/10.1007/s12021-015-9282-5
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author Ray, Subhasis
Chintaluri, Chaitanya
Bhalla, Upinder S.
Wójcik, Daniel K.
author_facet Ray, Subhasis
Chintaluri, Chaitanya
Bhalla, Upinder S.
Wójcik, Daniel K.
author_sort Ray, Subhasis
collection PubMed
description Data interchange is emerging as an essential aspect of modern neuroscience. In the areas of computational neuroscience and systems biology there are multiple model definition formats, which have contributed strongly to the development of an ecosystem of simulation and analysis tools. Here we report the development of the Neuroscience Simulation Data Format (NSDF) which extends this ecosystem to the data generated in simulations. NSDF is designed to store simulator output across scales: from multiscale chemical and electrical signaling models, to detailed single-neuron and network models, to abstract neural nets. It is self-documenting, efficient, modular, and scalable, both in terms of novel data types and in terms of data volume. NSDF is simulator-independent, and can be used by a range of standalone analysis and visualization tools. It may also be used to store variety of experimental data. NSDF is based on the widely used HDF5 (Hierarchical Data Format 5) specification and is open, platform-independent, and portable.
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spelling pubmed-48233482016-04-20 NSDF: Neuroscience Simulation Data Format Ray, Subhasis Chintaluri, Chaitanya Bhalla, Upinder S. Wójcik, Daniel K. Neuroinformatics Original Article Data interchange is emerging as an essential aspect of modern neuroscience. In the areas of computational neuroscience and systems biology there are multiple model definition formats, which have contributed strongly to the development of an ecosystem of simulation and analysis tools. Here we report the development of the Neuroscience Simulation Data Format (NSDF) which extends this ecosystem to the data generated in simulations. NSDF is designed to store simulator output across scales: from multiscale chemical and electrical signaling models, to detailed single-neuron and network models, to abstract neural nets. It is self-documenting, efficient, modular, and scalable, both in terms of novel data types and in terms of data volume. NSDF is simulator-independent, and can be used by a range of standalone analysis and visualization tools. It may also be used to store variety of experimental data. NSDF is based on the widely used HDF5 (Hierarchical Data Format 5) specification and is open, platform-independent, and portable. Springer US 2015-11-19 2016 /pmc/articles/PMC4823348/ /pubmed/26585711 http://dx.doi.org/10.1007/s12021-015-9282-5 Text en © The Author(s) 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Original Article
Ray, Subhasis
Chintaluri, Chaitanya
Bhalla, Upinder S.
Wójcik, Daniel K.
NSDF: Neuroscience Simulation Data Format
title NSDF: Neuroscience Simulation Data Format
title_full NSDF: Neuroscience Simulation Data Format
title_fullStr NSDF: Neuroscience Simulation Data Format
title_full_unstemmed NSDF: Neuroscience Simulation Data Format
title_short NSDF: Neuroscience Simulation Data Format
title_sort nsdf: neuroscience simulation data format
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823348/
https://www.ncbi.nlm.nih.gov/pubmed/26585711
http://dx.doi.org/10.1007/s12021-015-9282-5
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