Neuroscience Simulation Data Format
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README.md

nsdf

NSDF (Neuroscience Simulation Data Format) is a file format built on top of HDF5.

Although the design and development started with the aim of storing data generated from simulations in computational neuroscience, this format is generic enough that any time series data should fit in. Thus the actual application can be much broader than simulations in neuroscience.

  • NSDF is under development and we welcome feedback and suggestions from the community.

  • If you use nsdf for your research, please consider citing the article with NSDF specification:

    Ray, Subhasis, Chaitanya Chintaluri, Upinder S. Bhalla, and Daniel K. Wójcik. 2015. "NSDF: Neuroscience Simulation Data Format." Neuroinformatics, November, 1–21. doi:10.1007/s12021-015-9282-5.

Requirements

nsdf module works with h5py 2.3.1. Python 2.7 and numpy. The latest development version should also work with Python 3, but not fully tested yet.

To build the documentation you also need sphinx, sphinxcontrib-napoleon packages.

Installation

To install from PyPI use:

  1. If you have admin rights on a linux and want to install it for all users:

    sudo pip install nsdf

  2. If you don't have admin rights or want to install in your home directory

    pip install nsdf --user

To install the nsdf package from the source (available at "https://github.com/nsdf/nsdf"):

Open a terminal, cd to the top level directory (the one containing this file) and enter:

python setup.py install

To build the documentation, cd to doc directory and enter:

make html

This will create "_build" directory and the index of the docs will be in "_build/html/index.html". Or you can read the latest documentation built from git:master branch on nsdf.readthedocs.org.

Other Tools

dataviz A GUI utility for viewing HDF5 datasets.

Moogli Coming Soon. A Simulator independent visualization tool for neuronal simulations.

Credits

Subhasis Ray, Chaitanya Chintaluri, Upinder Bhalla and Daniel Wójcik have been designing the specification in collaboration.

Chaitanya is providing examples and use cases.

Subhasis is developing this Python module providing a high level API for reading and writing NSDF files.

We thank Aviral Goel, Johannes Rieke and Matteo Cantarelli for their critical input.

Zbigniew Jędrzejewski-Szmek contributed to structuring for packaging.