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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer US
2015
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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. |
format | Online Article Text |
id | pubmed-4823348 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Springer US |
record_format | MEDLINE/PubMed |
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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