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Neuroinformatics. 2016 Apr;14(2):147-67. doi: 10.1007/s12021-015-9282-5.

NSDF: Neuroscience Simulation Data Format.

Author information

1
National Center of Biological Sciences, Tata institute of Fundamental Research, Bangalore, India.
2
National Institutes of Health, Bethesda, MD, USA.
3
Nencki Institute of Experimental Biology, Warsaw, Poland.
4
National Center of Biological Sciences, Tata institute of Fundamental Research, Bangalore, India. bhalla@ncbs.res.in.
5
Nencki Institute of Experimental Biology, Warsaw, Poland. d.wojcik@nencki.gov.pl.

Abstract

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.

KEYWORDS:

Analysis tools; Data format; Data sharing; Simulations; Visualization

PMID:
26585711
PMCID:
PMC4823348
DOI:
10.1007/s12021-015-9282-5
[Indexed for MEDLINE]
Free PMC Article

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