3 ***********************************************
4 Welcome to the Debian Neuroscience Repository
5 ***********************************************
7 This repository provides mostly neuroscience-related packages to be used on
8 Debian_ systems (or Debian-derivatives like Ubuntu_). It contains both unofficial
9 or prospective packages which are not (yet) available from the main Debian_
10 archive, as well as backported or simply rebuilt packages also available
11 elsewhere. Please see the :ref:`faq` for more information about the goals of
14 This service is provided "as is". There is no guarantee that a package
15 works as expected, so use them at your own risk. If you encounter problems,
16 please `report <#contacts>`_ them.
18 Please |spread|, if you like it.
23 <a href="pkgs.html"><img border="0" src="_static/package.png" title="Software package list" /></a>
24 <a href="datasets.html"><img border="0" src="_static/datasets.png" title="Dataset package list" /></a>
25 <a href="vm.html"><img border="0" src="_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /></a>
26 <a href="debian/pool"><img border="0" src="_static/pool.png" title="Go to the package pool (deep and cold, only for experts)" /></a>
29 .. _Ubuntu: http://www.ubuntu.com
36 <script src="http://widgets.twimg.com/j/2/widget.js"></script>
47 background: '#898989',
51 background: '#ffffff',
65 }).render().setUser('NeuroDebian').start();
68 Follow us on twitter_ to subscribe to the NeuroDebian news.
70 .. _twitter: http://twitter.com/NeuroDebian
76 How to use this repository
77 ==========================
79 The easiest way to use this repository is to download an APT-configuration file
80 (`sources.list`). Simply choose your target distribution/release and download
81 the configuration for a mirror close to you (depending on your browser, you
82 might have to right-click and choose 'save as'). Once downloaded, put the file
83 in the `/etc/apt/sources.list.d/` directory on your system. Moving files in
84 this directory will require superuser privileges, therefore you should probably
85 download the file into a temporary directory and subsequently move it into
86 `/etc/apt/sources.list.d/`. APT-configurations are available for the following
87 releases and repository mirrors:
89 .. include:: sources_lists
92 Thanks to the following institutions and individuals for hosting a mirror:
94 * `Department of Psychological and Brain Sciences at Dartmouth College`_
95 `[us-nh]` (primary mirror)
96 * `Department of Experimental Psychology at the University of Magdeburg`_
98 * `Neurobot at Aristotle University of Thessaloniki, Greece`_ `[gr]`
99 * `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
102 If your are interested in mirroring the repository, please see the :ref:`faq`.
104 .. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
105 .. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
106 .. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
107 .. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
109 Once this is done, you have to update the package index. Use your favorite
110 package manager, e.g. synaptic, adept, or whatever you like. In the terminal
111 you can use :command:`aptitude` to achieve the same::
115 Now, you can proceed to install packages, e.g.::
117 sudo aptitude install lipsia
120 Not every package is available for all distributions/releases. For information
121 about which package version is available for which release and architecture,
122 please have a look at the corresponding package pages.
125 Package authentication
126 ----------------------
128 When you start using this repository, you probably get warning messages
131 The following signatures couldn't be verified because
132 the public key is not available.
134 Or you will be asked questions like this over and over::
136 WARNING: The following packages cannot be authenticated!
138 Install these packages without verification [y/N]?
140 This is because your APT installation initially does not know the GPG
141 key that is used to sign the release files of this repository. It is easy to
142 make APT happy again:
144 1. Get the key. Either download the `repository key from here
145 <_static/neuro.debian.net.asc>`_
146 or fetch it from http://wwwkeys.pgp.net (2649A5A9).
148 2. Now feed the key into APT by invoking::
152 Where `#file#` has to be replaced with the location of the key file you just
153 downloaded. You need to have superuser-privileges to do this (either do it
154 as root or use sudo).
157 .. _chap_installation:
165 If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
166 provided as a convenient testing and evaluation environment. After a few
167 simple steps to setup the virtual machine, you will be able to use NeuroDebian_
168 as an integral part of your existing working environment without any sacrifice.
169 The virtual machine is also a suitable environment to temporarily deploy
170 neuroscience software on machines running other operating systems, e.g. for the
171 purpose of teaching a neuroimaging data analysis course in a multipurpose
178 Having been exposed to the wonders of NeuroDebian_ you are no longer
179 satisfied with your previous choice of operating system? We would
180 recommend installing Debian_ to replace or complement (dual-boot) your
181 existing OS. Please visit `"Getting Debian"
182 <http://www.debian.org/distrib/>`_ to obtain the images for your
183 hardware architecture and then simply add |repos|.
192 Our main goal is to provide neuroscience FOSS_ for Debian_. Thus the
193 whole project would not be possible without the work of over 3,000
194 Debian_ developers and contributors who are as enthusiastically pursuing
195 a similar goal. To add our share -- Debian_ packages of FOSS_ for
196 neuroscience research -- the `Experimental Psychology Debian packaging
197 project <http://alioth.debian.org/projects/pkg-exppsy>`_ was created
198 to formally join the forces of
200 * `Michael Hanke <http://mih.voxindeserto.de>`_
201 * `Yaroslav Halchenko <http://www.onerussian.com>`_
203 A number of packages that are now available from the NeuroDebian repository
204 were not packaged by our team, but similar Debian teams. Therefore we want to
205 express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
208 .. _FOSS: http://en.wikipedia.org/wiki/Free_and_open_source_software
214 `Email us directly <team@neuro.debian.net>`_ with any "private"
215 communication. Otherwise please use our public mailing lists, which
216 exist not only to provide user-support but also to establish
217 communication channels within the NeuroDebian community
219 * neurodebian-users_: Discussions and support of NeuroDebian users
221 * neurodebian-upstream_: General discussions and knowledge sharing
222 among developers of the neuroscience software. We will also use it
223 to update you with summaries of recent relevant developments in
226 * neurodebian-devel_: Technical mailing list for discussions on
227 NeuroDebian development
229 .. _neurodebian-users: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users
230 .. _neurodebian-devel: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel
231 .. _neurodebian-upstream: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-upstream
242 .. probably should be purged altogether
252 .. include:: links_names.rst
253 .. include:: substitutions.rst