NeuroTools

NeuroTools is a collection of tools for representing and analyzing neuroscientific data.

NeuroTools is written in Python, and works best with PyNN, or one of the growing list of simulation engines with a Python front-end such as NEURON, NEST, PCSIM, FACETS Neuromorphic VLSI, Brian, MOOSE/GENESIS, Neurospaces/GENESIS. NeuroTools provides modules to facilitate simulation setup, parameterization and instrumentation, and data management, analysis and visualization. The data-related tools are equally suited to analysis of experimental data, although that is not the primary motivation for their development.

NeuroTools aims to:

1. increase the productivity of individual modellers by automating, simplifying, and establishing best-practices for common tasks,
2. increase the productivity of the neuroscience modelling community by reducing the amount of code duplication across simulation communities,
3. increase the reliability of data analysis tools leveraging Linus's law: "given enough eyeballs, all bugs are shallow."

Code status

This code is considered to be mature and will not evolve - we will only focus on bug fixes.

Development of a new analysis library takes place @ https://github.com/NeuralEnsemble/elephant

Contributing to NeuroTools

If you are interested in participating in NeuroTools development, please see the webpage at http://neuralensemble.org/NeuroTools

Related projects

NeuroTools has evolved in different flavours:

• a legacy version @ https://neuralensemble.kip.uni-heidelberg.de/svn/NeuroTools
• a fork by Trevor Bekolay: https://github.com/tbekolay/neurotools
• another fork (version 0.2.0) : https://github.com/meduz/NeuroTools

Installation

To install use:

pip install NeuroTools

For installation instructions, see doc/source/install.rst

Documentation

For documentation see the doc folder or http://packages.python.org/NeuroTools

For examples see the examples folder.

More information

• Home page: http://neuralensemble.org/NeuroTools
• Mailing list: https://groups.google.com/forum/?fromgroups#!forum/neuralensemble
• Documentation: http://packages.python.org/neo/
• Bug reports: https://github.com/NeuralEnsemble/NeuroTools/issues

License

Copyright (C) 2008 Daniel Bruederle, Andrew Davison, Jens Kremkow Laurent Perrinet, Michael Schmuker, Eilif Muller, Eric Mueller, Pierre Yger

NeuroTools is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

The GNU General Public License does not permit this software to be redistributed in proprietary programs.

See LICENSE.