Neuroscience information exchange format
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README.md

Build Status Build status Coverage Status

About NIX

The NIX project (previously called Pandora) started as an initiative of the Electrophysiology Task Force which is part of the INCF Data sharing Program. As such the project aims to develop standardized methods and models for storing electrophysiology and other neuroscience data together with their metadata in one common file format based on HDF5.

See the wiki for more information

Development Status

The NIX project is now in a Beta stage and should not be seen as a final product. However, the data model as well as the HDF schema and the C++ api are feature complete and should undergo little to no changes in the future.

Getting Started (Linux)

Debian PPA

You can get a ready to install package for Ubuntu "trusty". You have to add & install the following software source to your system:

deb http://ppa.launchpad.net/gnode/nix/ubuntu trusty main
deb-src http://ppa.launchpad.net/gnode/nix/ubuntu trusty main

by executing

sudo add-apt-repository ppa:gnode/nix
sudo apt-get update
sudo apt-get install libnix-dev

Build NIX under Ubuntu 14.04

Dependencies

In order to build the NIX library a recent C++11 compatible compiler is needed (g++ >= 4.8, clang >= 3.4) as well as the build tool CMake (>= 2.8.9). Further nix depends on the following third party libraries:

  • HDF5 (version 1.8.13 or higher)
  • Boost (version 1.49 or higher)
  • CppUnit (version 1.12.1 or higher)

Instructions

# 1 install dependencies
sudo apt-get install libboost-all-dev libhdf5-serial-dev libcppunit-dev cmake build-essential

**Note:** If the standard version of the boost libraries in your distribution is less than 1.49,
# manually install a version larger than 1.49 from the launchad (https://launchpad.net/~boost-latest/+archive/ubuntu/ppa)

# 2 clone NIX
git clone https://github.com/G-Node/nix
cd nix

# 3 make a build dir and build nix
mkdir build
cd build
cmake ..
make all

# 4 run the unit tests
ctest

# 5 install
sudo make install

In case building nix fails because libboost-*** libraries are not found try the following:

# 3 make a build dir and build nix
mkdir build
cd build
cmake -DBoost_NO_BOOST_CMAKE=TRUE ..
make all

NIX with Docker

To develop with NIX inside the Linux Container system Docker you can use the images available under the balint42/nix repository on the public Docker Hub. Further instructions on how to use the images are on the Docker repository. Further instructions for Docker can be found on their site.

Getting Started (MacOS X)

The easiest way to get NIX is via homebrew. We are included in homebrew science as nixio. Install nix, including missing dependencies, with:

brew install homebrew/science/nixio

# OR: tap into homebrew-science
brew tap homebrew/science
brew install nixio

# If you want the latest development version:
# NB: replace 'install', with 'reinstall' to upgrade
#     an existing installation
brew install --HEAD nixio

Getting Started (Windows)

Windows Installer

You can get a windows installer for both, 32- and 64-bit.

Build NIX under Windows

To build NIX under windows follow the guide provided under: Win32.md

NIX API Documentation

The API documentation can be found here

NIX Tutorials

If you want to learn about the features of the NIX data model and how it can be used to represent various kinds of data you may want to check out the tutorials. We have assembled a set of tutorial here using the python wrapper.