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="blog/index.html"><img border="0" src="_static/rssfeeds.png" title="NeuroDebian Insider Blog" /></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 For more news and information see our :ref:`blog <blog>`. Older news items are
57 available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to
58 subscribe to the NeuroDebian news.
60 .. _identi.ca: http://identi.ca/neurodebian
61 .. _twitter: http://twitter.com/NeuroDebian
67 How to use this repository
68 ==========================
70 To enable the NeuroDebian repository on your system, select your Debian or
71 Ubuntu release and a repository mirror from the lists below. Upon selection
72 a short command snippet will be displayed that can be copied and pasted into
73 a terminal session. These commands will configure the system package manager
74 with the NeuroDebian repository key and package source information.
76 .. include:: sources_lists
78 Once this is done, you have to update the package index and you are ready to
79 install packages. Use your favorite package manager, e.g. synaptic, adept. In
80 the terminal you can use :command:`apt-get`::
83 sudo apt-get install mricron
87 Not every package is available for all distributions/releases. For information
88 about which package version is available for which release and architecture,
89 please have a look at the corresponding package pages.
92 .. _chap_installation:
94 Ways to use NeuroDebian
95 =======================
100 If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
101 provided as a convenient testing and evaluation environment. After a few
102 simple steps to setup the virtual machine, you will be able to use NeuroDebian_
103 as an integral part of your existing working environment without any sacrifice.
104 The virtual machine is also a suitable environment to temporarily deploy
105 neuroscience software on machines running other operating systems, e.g. for the
106 purpose of teaching a neuroimaging data analysis course in a multipurpose
113 Having been exposed to the wonders of NeuroDebian_ you are no longer
114 satisfied with your previous choice of operating system? We would
115 recommend installing Debian_ to replace or complement (dual-boot) your
116 existing OS. Please visit `"Getting Debian"
117 <http://www.debian.org/distrib/>`_ to obtain the images for your
118 hardware architecture and then simply add |repos|.
127 Our main goal is to provide neuroscience FOSS_ for Debian_. Thus the
128 whole project would not be possible without the work of over 3,000
129 Debian_ developers and contributors who are as enthusiastically pursuing
130 a similar goal. To add our share -- Debian_ packages of FOSS_ for
131 neuroscience research -- the `Experimental Psychology Debian packaging
132 project <http://alioth.debian.org/projects/pkg-exppsy>`_ was created
133 to formally join the forces of
135 * `Michael Hanke <http://mih.voxindeserto.de>`_
136 * `Yaroslav Halchenko <http://www.onerussian.com>`_
138 A number of packages that are now available from the NeuroDebian repository
139 were not packaged by our team, but similar Debian teams. Therefore we want to
140 express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
148 `Email us directly <team@neuro.debian.net>`_ with any "private"
149 communication. Otherwise please use our public mailing lists, which
150 exist not only to provide user-support but also to establish
151 communication channels within the NeuroDebian community
153 * neurodebian-users_: Discussions and support of NeuroDebian users
155 * neurodebian-upstream_: General discussions and knowledge sharing
156 among developers of the neuroscience software. We will also use it
157 to update you with summaries of recent relevant developments in
160 * neurodebian-devel_: Technical mailing list for discussions on
161 NeuroDebian development
163 You are welcome also to join #neurodebian IRC room on OFTC network if
164 you have quick questions or want to join a live discussion.
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 Halchenko, Y. O. (2011). `π's in Debian or Scientific Debian: NumPy, SciPy and beyond
198 <_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
199 *Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
202 Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
203 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
204 *Frontiers in Neuroinformatics, 5:8*.
206 Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
207 platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
208 *Poster presented at the annual meeting of the Organisation for Human Brain
209 Mapping*, Quebec City, Canada.
211 Hanke, M. (2011). `Integrating Condor into the Debian operating system
212 <_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
213 *Talk given at* `CondorWeek 2011
214 <http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
215 Madison, Wisconsin, USA.
217 Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
218 SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
219 Neuroscience*, San Diego, USA.
221 Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
222 (2010). `Having trouble getting your Nature paper? Maybe you are not using the
223 right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster presented at the
224 annual meeting of the Society for Neuroscience*, San Diego, USA.
226 Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
227 neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
228 *Talk given at* DebConf10_, New York City, USA. [video:
229 `low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
230 `high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
232 Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
233 efficiency in cognitive neuroscience research with NeuroDebian
234 <_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
235 meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
237 Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
238 statistical learning, and open-source software to make research more
239 efficient, more open, and more fun
240 <_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
241 `Dartmouth College`_, New Hampshire, USA.
243 .. _DebConf10: http://debconf10.debconf.org/
244 .. _Dartmouth College: http://www.dartmouth.edu/
260 .. probably should be purged altogether
272 .. include:: link_names.txt
273 .. include:: substitutions.txt