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="pkglists/pkgs-by_release-datasets_(data).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>
34 <a href="feeds/blog.xml"><img border="0" src="_static/rssfeeds.png" title="NeuroDebian Insider feed" /></a>
37 .. _Ubuntu: http://www.ubuntu.com
46 <script src="_static/jquery.livetwitter.min.js"></script>
47 <div id="identica_widget"></div>
48 <script type="text/javascript">
49 $("#identica_widget").liveTwitter('neurodebian',
50 {service: 'identi.ca',
51 mode: 'user_timeline',
56 Older news items are available on identi.ca_. Follow us on identi.ca_
57 (preferred) or twitter_ to subscribe to the NeuroDebian news.
59 .. _identi.ca: http://identi.ca/neurodebian
60 .. _twitter: http://twitter.com/NeuroDebian
66 How to use this repository
67 ==========================
69 To enable the NeuroDebian repository on your system, select your Debian or
70 Ubuntu release and a repository mirror from the lists below. Upon selection
71 a short command snippet will be displayed that can be copied and pasted into
72 a terminal session. These commands will configure the system package manager
73 with the NeuroDebian repository key and package source information.
75 .. include:: sources_lists
77 Once this is done, you have to update the package index. Use your favorite
78 package manager, e.g. synaptic, adept. In the terminal you can use
79 :command:`apt-get` to achieve this::
83 Now, you can install packages, e.g.::
85 sudo apt-get install mricron
89 Not every package is available for all distributions/releases. For information
90 about which package version is available for which release and architecture,
91 please have a look at the corresponding package pages.
94 .. _chap_installation:
96 Ways to use NeuroDebian
97 =======================
102 If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
103 provided as a convenient testing and evaluation environment. After a few
104 simple steps to setup the virtual machine, you will be able to use NeuroDebian_
105 as an integral part of your existing working environment without any sacrifice.
106 The virtual machine is also a suitable environment to temporarily deploy
107 neuroscience software on machines running other operating systems, e.g. for the
108 purpose of teaching a neuroimaging data analysis course in a multipurpose
115 Having been exposed to the wonders of NeuroDebian_ you are no longer
116 satisfied with your previous choice of operating system? We would
117 recommend installing Debian_ to replace or complement (dual-boot) your
118 existing OS. Please visit `"Getting Debian"
119 <http://www.debian.org/distrib/>`_ to obtain the images for your
120 hardware architecture and then simply add |repos|.
129 Our main goal is to provide neuroscience FOSS_ for Debian_. Thus the
130 whole project would not be possible without the work of over 3,000
131 Debian_ developers and contributors who are as enthusiastically pursuing
132 a similar goal. To add our share -- Debian_ packages of FOSS_ for
133 neuroscience research -- the `Experimental Psychology Debian packaging
134 project <http://alioth.debian.org/projects/pkg-exppsy>`_ was created
135 to formally join the forces of
137 * `Michael Hanke <http://mih.voxindeserto.de>`_
138 * `Yaroslav Halchenko <http://www.onerussian.com>`_
140 A number of packages that are now available from the NeuroDebian repository
141 were not packaged by our team, but similar Debian teams. Therefore we want to
142 express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
150 `Email us directly <team@neuro.debian.net>`_ with any "private"
151 communication. Otherwise please use our public mailing lists, which
152 exist not only to provide user-support but also to establish
153 communication channels within the NeuroDebian community
155 * neurodebian-users_: Discussions and support of NeuroDebian users
157 * neurodebian-upstream_: General discussions and knowledge sharing
158 among developers of the neuroscience software. We will also use it
159 to update you with summaries of recent relevant developments in
162 * neurodebian-devel_: Technical mailing list for discussions on
163 NeuroDebian development
169 We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
170 Italian espresso <coffeeart>`.
172 .. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
174 Thanks to the following institutions and individuals for hosting a mirror:
176 * `Department of Psychological and Brain Sciences at Dartmouth College`_
177 *[us-nh]* (primary mirror)
178 * `Department of Experimental Psychology at the University of Magdeburg`_
180 * `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
181 * `Paul Ivanov`_ *[us-ca]*
182 * `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
185 If your are interested in mirroring the repository, please see the :ref:`faq`.
187 .. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
188 .. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
189 .. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
190 .. _Paul Ivanov: http://www.pirsquared.org
191 .. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
197 Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
198 SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
199 Neuroscience*, San Diego, USA.
201 Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
202 (2010). `Having trouble getting your Nature paper? Maybe you are not using the
203 right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster to be presented at the
204 annual meeting of the Society for Neuroscience*, San Diego, USA.
206 Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
207 neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
208 *Talk given at* DebConf10_, New York City, USA. [video:
209 `low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
210 `high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
212 Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
213 efficiency in cognitive neuroscience research with NeuroDebian
214 <_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
215 meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
217 Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
218 statistical learning, and open-source software to make research more
219 efficient, more open, and more fun
220 <_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
221 `Dartmouth College`_, New Hampshire, USA.
223 .. _DebConf10: http://debconf10.debconf.org/
224 .. _Dartmouth College: http://www.dartmouth.edu/
239 .. probably should be purged altogether
251 .. include:: link_names.txt
252 .. include:: substitutions.txt