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 Take a look at the :ref:`list of our current and planned projects <projects>` if
17 you want to get involved. If you appreciate this service, please |spread|.
21 This service is provided "as is". There is no guarantee that a package
22 works as expected, so use them at your own risk. If you encounter problems,
23 please `report <#contacts>`_ them.
29 <a href="pkgs.html"><img border="0" src="_static/package.png" title="Software package list" /></a>
30 <a href="datasets.html"><img border="0" src="_static/datasets.png" title="Dataset package list" /></a>
31 <a href="vm.html"><img border="0" src="_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /></a>
32 <a href="debian/pool"><img border="0" src="_static/pool.png" title="Go to the package pool (deep and cold, only for experts)" /></a>
33 <a href="projects.html"><img border="0" src="_static/workarea.png" title="Current and planned projects: Get involved!" /></a>
36 .. _Ubuntu: http://www.ubuntu.com
45 <script src="http://widgets.twimg.com/j/2/widget.js"></script>
56 background: '#898989',
60 background: '#ffffff',
74 }).render().setUser('NeuroDebian').start();
77 Follow us on identi.ca_ or twitter_ to subscribe to the NeuroDebian news.
79 .. _identi.ca: http://identi.ca/neurodebian
80 .. _twitter: http://twitter.com/NeuroDebian
86 How to use this repository
87 ==========================
89 The easiest way to use this repository is to download an APT-configuration file
90 (`sources.list`). Simply choose your target distribution/release and download
91 the configuration for a mirror close to you (depending on your browser, you
92 might have to right-click and choose 'save as'). Once downloaded, put the file
93 in the `/etc/apt/sources.list.d/` directory on your system. Moving files in
94 this directory will require superuser privileges, therefore you should probably
95 download the file into a temporary directory and subsequently move it into
96 `/etc/apt/sources.list.d/`. APT-configurations are available for the following
97 releases and repository mirrors:
99 .. include:: sources_lists
102 Thanks to the following institutions and individuals for hosting a mirror:
104 * `Department of Psychological and Brain Sciences at Dartmouth College`_
105 *[us-nh]* (primary mirror)
106 * `Department of Experimental Psychology at the University of Magdeburg`_
108 * `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
109 * `Paul Ivanov`_ *[us-ca]*
110 * `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
113 If your are interested in mirroring the repository, please see the :ref:`faq`.
115 .. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
116 .. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
117 .. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
118 .. _Paul Ivanov: http://www.pirsquared.org
119 .. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
121 Once this is done, you have to update the package index. Use your favorite
122 package manager, e.g. synaptic, adept, or whatever you like. In the terminal
123 you can use :command:`aptitude` to achieve the same::
127 Now, you can proceed to install packages, e.g.::
129 sudo aptitude install lipsia
132 Not every package is available for all distributions/releases. For information
133 about which package version is available for which release and architecture,
134 please have a look at the corresponding package pages.
136 After this initial setup you probably also want to configure your package
137 manager to recognize the NeuroDebian archive key. With this key the package
138 manager can verify that packages haven't been modified and are identical with
139 the ones in the main NeuroDebian archive, regardless of which mirror you
140 downloaded them from. The NeuroDebian key id is **2649A5A9**. If you need further
141 help setting up package authentication, please take a look at
142 :ref:`corresponding FAQ <sec_pkg_authentication>`.
145 .. _chap_installation:
147 Ways to use NeuroDebian
148 =======================
153 If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
154 provided as a convenient testing and evaluation environment. After a few
155 simple steps to setup the virtual machine, you will be able to use NeuroDebian_
156 as an integral part of your existing working environment without any sacrifice.
157 The virtual machine is also a suitable environment to temporarily deploy
158 neuroscience software on machines running other operating systems, e.g. for the
159 purpose of teaching a neuroimaging data analysis course in a multipurpose
166 Having been exposed to the wonders of NeuroDebian_ you are no longer
167 satisfied with your previous choice of operating system? We would
168 recommend installing Debian_ to replace or complement (dual-boot) your
169 existing OS. Please visit `"Getting Debian"
170 <http://www.debian.org/distrib/>`_ to obtain the images for your
171 hardware architecture and then simply add |repos|.
180 Our main goal is to provide neuroscience FOSS_ for Debian_. Thus the
181 whole project would not be possible without the work of over 3,000
182 Debian_ developers and contributors who are as enthusiastically pursuing
183 a similar goal. To add our share -- Debian_ packages of FOSS_ for
184 neuroscience research -- the `Experimental Psychology Debian packaging
185 project <http://alioth.debian.org/projects/pkg-exppsy>`_ was created
186 to formally join the forces of
188 * `Michael Hanke <http://mih.voxindeserto.de>`_
189 * `Yaroslav Halchenko <http://www.onerussian.com>`_
191 A number of packages that are now available from the NeuroDebian repository
192 were not packaged by our team, but similar Debian teams. Therefore we want to
193 express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
201 `Email us directly <team@neuro.debian.net>`_ with any "private"
202 communication. Otherwise please use our public mailing lists, which
203 exist not only to provide user-support but also to establish
204 communication channels within the NeuroDebian community
206 * neurodebian-users_: Discussions and support of NeuroDebian users
208 * neurodebian-upstream_: General discussions and knowledge sharing
209 among developers of the neuroscience software. We will also use it
210 to update you with summaries of recent relevant developments in
213 * neurodebian-devel_: Technical mailing list for discussions on
214 NeuroDebian development
220 We are grateful to Jim Haxby for his continued support and :ref:`endless supply of
221 Italian espresso <coffeeart>`.
227 Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
228 SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
229 Neuroscience*, San Diego, USA.
231 Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
232 (2010). `Having trouble getting your Nature paper? Maybe you are not using the
233 right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster to be presented at the
234 annual meeting of the Society for Neuroscience*, San Diego, USA.
236 Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
237 neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
238 *Talk given at* DebConf10_, New York City, USA. [video:
239 `low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
240 `high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
242 Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
243 efficiency in cognitive neuroscience research with NeuroDebian
244 <_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
245 meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
247 Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
248 statistical learning, and open-source software to make research more
249 efficient, more open, and more fun
250 <_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
251 `Dartmouth College`_, New Hampshire, USA.
253 .. _DebConf10: http://debconf10.debconf.org/
254 .. _Dartmouth College: http://www.dartmouth.edu/
269 .. probably should be purged altogether
281 .. include:: link_names.txt
282 .. include:: substitutions.txt