3 ***********************************************
4 Welcome to the Debian Neuroscience Repository
5 ***********************************************
10 This repository provides mostly neuroscience-related packages to be used on
11 Debian_ systems (or Debian-derivatives like Ubuntu_). It contains both unofficial
12 or prospective packages which are not (yet) available from the main Debian_
13 archive, as well as backported or simply rebuilt packages also available
14 elsewhere. Please see the :ref:`faq` for more information about the goals of
15 this project, and :ref:`read what people say about it <testimonials>`.
16 If you appreciate this service, please |spread|.
20 This service is provided "as is". There is no guarantee that a package
21 works as expected, so use them at your own risk. If you encounter problems,
22 please `report <#contacts>`_ them.
28 <a href="pkgs.html"><img border="0" src="_static/package.png" title="Software package list" /></a>
29 <a href="datasets.html"><img border="0" src="_static/datasets.png" title="Dataset package list" /></a>
30 <a href="vm.html"><img border="0" src="_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /></a>
31 <a href="debian/pool"><img border="0" src="_static/pool.png" title="Go to the package pool (deep and cold, only for experts)" /></a>
34 .. _Ubuntu: http://www.ubuntu.com
43 <script src="http://widgets.twimg.com/j/2/widget.js"></script>
54 background: '#898989',
58 background: '#ffffff',
72 }).render().setUser('NeuroDebian').start();
75 Follow us on twitter_ to subscribe to the NeuroDebian news.
77 .. _twitter: http://twitter.com/NeuroDebian
83 How to use this repository
84 ==========================
86 The easiest way to use this repository is to download an APT-configuration file
87 (`sources.list`). Simply choose your target distribution/release and download
88 the configuration for a mirror close to you (depending on your browser, you
89 might have to right-click and choose 'save as'). Once downloaded, put the file
90 in the `/etc/apt/sources.list.d/` directory on your system. Moving files in
91 this directory will require superuser privileges, therefore you should probably
92 download the file into a temporary directory and subsequently move it into
93 `/etc/apt/sources.list.d/`. APT-configurations are available for the following
94 releases and repository mirrors:
96 .. include:: sources_lists
99 Thanks to the following institutions and individuals for hosting a mirror:
101 * `Department of Psychological and Brain Sciences at Dartmouth College`_
102 *[us-nh]* (primary mirror)
103 * `Department of Experimental Psychology at the University of Magdeburg`_
105 * `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
106 * `Paul Ivanov`_ *[us-ca]*
107 * `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
110 If your are interested in mirroring the repository, please see the :ref:`faq`.
112 .. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
113 .. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
114 .. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
115 .. _Paul Ivanov: http://www.pirsquared.org
116 .. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
118 Once this is done, you have to update the package index. Use your favorite
119 package manager, e.g. synaptic, adept, or whatever you like. In the terminal
120 you can use :command:`aptitude` to achieve the same::
124 Now, you can proceed to install packages, e.g.::
126 sudo aptitude install lipsia
129 Not every package is available for all distributions/releases. For information
130 about which package version is available for which release and architecture,
131 please have a look at the corresponding package pages.
133 After this initial setup you probably also want to configure your package
134 manager to recognize the NeuroDebian archive key. With this key the package
135 manager can verify that packages haven't been modified and are identical with
136 the ones in the main NeuroDebian archive, regardless of which mirror you
137 downloaded them from. The NeuroDebian key id is **2649A5A9**. If you need further
138 help setting up package authentication, please take a look at
139 :ref:`corresponding FAQ <sec_pkg_authentication>`.
142 .. _chap_installation:
144 Ways to use NeuroDebian
145 =======================
150 If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
151 provided as a convenient testing and evaluation environment. After a few
152 simple steps to setup the virtual machine, you will be able to use NeuroDebian_
153 as an integral part of your existing working environment without any sacrifice.
154 The virtual machine is also a suitable environment to temporarily deploy
155 neuroscience software on machines running other operating systems, e.g. for the
156 purpose of teaching a neuroimaging data analysis course in a multipurpose
163 Having been exposed to the wonders of NeuroDebian_ you are no longer
164 satisfied with your previous choice of operating system? We would
165 recommend installing Debian_ to replace or complement (dual-boot) your
166 existing OS. Please visit `"Getting Debian"
167 <http://www.debian.org/distrib/>`_ to obtain the images for your
168 hardware architecture and then simply add |repos|.
177 Our main goal is to provide neuroscience FOSS_ for Debian_. Thus the
178 whole project would not be possible without the work of over 3,000
179 Debian_ developers and contributors who are as enthusiastically pursuing
180 a similar goal. To add our share -- Debian_ packages of FOSS_ for
181 neuroscience research -- the `Experimental Psychology Debian packaging
182 project <http://alioth.debian.org/projects/pkg-exppsy>`_ was created
183 to formally join the forces of
185 * `Michael Hanke <http://mih.voxindeserto.de>`_
186 * `Yaroslav Halchenko <http://www.onerussian.com>`_
188 A number of packages that are now available from the NeuroDebian repository
189 were not packaged by our team, but similar Debian teams. Therefore we want to
190 express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
193 .. _FOSS: http://en.wikipedia.org/wiki/Free_and_open_source_software
200 `Email us directly <team@neuro.debian.net>`_ with any "private"
201 communication. Otherwise please use our public mailing lists, which
202 exist not only to provide user-support but also to establish
203 communication channels within the NeuroDebian community
205 * neurodebian-users_: Discussions and support of NeuroDebian users
207 * neurodebian-upstream_: General discussions and knowledge sharing
208 among developers of the neuroscience software. We will also use it
209 to update you with summaries of recent relevant developments in
212 * neurodebian-devel_: Technical mailing list for discussions on
213 NeuroDebian development
215 .. _neurodebian-users: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users
216 .. _neurodebian-devel: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel
217 .. _neurodebian-upstream: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-upstream
223 We are grateful to Jim Haxby for his continued support and :ref:`endless supply of
224 Italian espresso <coffeeart>`.
230 Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
231 (2010). `Having trouble getting your Nature paper? Maybe you are not using the
232 right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster to be presented at the
233 anual meeting of the Society for Neuroscience*, San Diego, USA.
235 Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
236 neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
237 *Talk given at* DebConf10_, New York City, USA. [video:
238 `low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
239 `high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
241 Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
242 efficiency in cognitive neuroscience research with NeuroDebian
243 <_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
244 meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
246 Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
247 statistical learning, and open-source software to make research more
248 efficient, more open, and more fun
249 <_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
250 `Dartmouth College`_, New Hampshire, USA.
252 .. _DebConf10: http://debconf10.debconf.org/
253 .. _Dartmouth College: http://www.dartmouth.edu/
267 .. probably should be purged altogether
278 .. include:: link_names.txt
279 .. include:: substitutions.txt