3 ***************************************************
4 Welcome to the Ultimate Platform for Neuroscience
5 ***************************************************
10 The NeuroDebian project provides a turnkey platform for neuroscience
11 through integrating of related software within the Debian_ operating
12 system. If you are using neuroscience-related software which
13 comes with you installation of Debian_ or its derivative, such as
14 Ubuntu_, good chance is that you are already *using NeuroDebian*.
16 This website provides an additional repository with both unofficial
17 or prospective packages which are not (yet) available from the main
18 Debian_ archive, as well as backported or simply rebuilt newest
20 NeuroDebian serves as an "upstream" to some :ref:`derivative
21 <chap_derivatives>` projects.
22 Please see the :ref:`faq` for more information
23 about the goals of this project, and :ref:`read what people say about
24 it <testimonials>`. Take a look at the :ref:`list of our current and
25 planned projects <projects>` if you want to get involved. If you
26 appreciate this service, please |spread|.
27 This service is provided "as is". There is no guarantee that a package
28 works as expected, so use them at your own risk. If you encounter problems,
29 please `report <#contacts>`_ them.
34 <a href="pkgs.html"><img border="0" src="_static/package.png" title="Software package list" /></a>
35 <a href="pkglists/pkgs-by_release-datasets_(data).html"><img border="0" src="_static/datasets.png" title="Dataset package list" /></a>
36 <a href="vm.html"><img border="0" src="_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /></a>
37 <a href="debian/pool"><img border="0" src="_static/pool.png" title="Go to the package pool (deep and cold, only for experts)" /></a>
38 <a href="projects.html"><img border="0" src="_static/workarea.png" title="Current and planned projects: Get involved!" /></a>
39 <a href="derivatives.html"><img border="0" src="_static/derivatives.png" title="NeuroDebian Derivatives" /></a>
40 <a href="blog/index.html"><img border="0" src="_static/rssfeeds.png" title="NeuroDebian Insider Blog" /></a>
43 .. _Ubuntu: http://www.ubuntu.com
52 <script src="_static/jquery.livetwitter.min.js"></script>
53 <div id="identica_widget"></div>
54 <script type="text/javascript">
55 $("#identica_widget").liveTwitter('neurodebian',
56 {service: 'identi.ca',
57 mode: 'user_timeline',
62 For more news and information see our :ref:`blog <blog>`. Older news items are
63 available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to
64 subscribe to the NeuroDebian news.
66 .. _identi.ca: http://identi.ca/neurodebian
67 .. _twitter: http://twitter.com/NeuroDebian
73 How to use this repository
74 ==========================
76 To enable the NeuroDebian repository on your system, select your Debian or
77 Ubuntu release and a repository mirror from the lists below. Upon selection
78 a short command snippet will be displayed that can be copied and pasted into
79 a terminal session. These commands will configure the system package manager
80 with the NeuroDebian repository key and package source information.
82 .. include:: sources_lists
84 Once this is done, you have to update the package index and you are ready to
85 install packages. Use your favorite package manager, e.g. synaptic, adept. In
86 the terminal you can use :command:`apt-get`::
89 sudo apt-get install mricron
93 Not every package is available for all distributions/releases. For information
94 about which package version is available for which release and architecture,
95 please have a look at the corresponding package pages.
99 <p><img border="0" src="_files/nd_subscriptionstats.png" title="Statistics of new repository subscriptions for all supported releases. Note: subscription is only done once per machine." /></p>
104 We encourage you to participate in the `popularity
105 contest <http://popcon.debian.org>`_ (popcon), which anonymously
106 collects the list of packages you installed/use on your system.
107 Collecting such statistics is of particular importance for research
108 software projects as a prove of an existing user-base. If upon
109 installation of the system you rejected the invitation to participate
110 you can always change your decision by running::
112 sudo dpkg-reconfigure popularity-contest
116 If you are deploying multiple systems through cloning, to not have
117 all systems considered as one, it would be necessary to re-generate
118 the random MY_HOSTID. Following commands ran as root should do it
119 (as root) without any interactive dialog::
121 sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
122 DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
124 In addition to popcon pages for your "core" distribution (e.g. `Debian
125 <http://popcon.debian.org/>`__ or `Ubuntu
126 <http://popcon.ubuntu.com/>`__) you can see/get statistics for
127 submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
128 know that you are already contributing back to the community.
130 .. _chap_installation:
132 Ways to use NeuroDebian
133 =======================
138 If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
139 provided as a convenient testing and evaluation environment. After a few
140 simple steps to setup the virtual machine, you will be able to use NeuroDebian_
141 as an integral part of your existing working environment without any sacrifice.
142 The virtual machine is also a suitable environment to temporarily deploy
143 neuroscience software on machines running other operating systems, e.g. for the
144 purpose of teaching a neuroimaging data analysis course in a multipurpose
151 Having been exposed to the wonders of NeuroDebian_ you are no longer
152 satisfied with your previous choice of operating system? We would
153 recommend installing Debian_ to replace or complement (dual-boot) your
154 existing OS. Please visit `"Getting Debian"
155 <http://www.debian.org/distrib/>`_ to obtain the images for your
156 hardware architecture and then simply add |repos|.
165 Our main goal is to provide neuroscience FOSS_ for Debian_. Thus the
166 whole project would not be possible without the work of over 3,000
167 Debian_ developers and contributors who are as enthusiastically pursuing
168 a similar goal. To add our share -- Debian_ packages of FOSS_ for
169 neuroscience research -- the `Experimental Psychology Debian packaging
170 project <http://alioth.debian.org/projects/pkg-exppsy>`_ was created
171 to formally join the forces of
173 * `Michael Hanke <http://mih.voxindeserto.de>`_
174 * `Yaroslav Halchenko <http://www.onerussian.com>`_
176 A number of packages that are now available from the NeuroDebian repository
177 were not packaged by our team, but similar Debian teams. Therefore we want to
178 express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
186 `Email us directly <team@neuro.debian.net>`_ with any "private"
187 communication. Otherwise please use our public mailing lists, which
188 exist not only to provide user-support but also to establish
189 communication channels within the NeuroDebian community
191 * neurodebian-users_: Discussions and support of NeuroDebian users
193 * neurodebian-upstream_: General discussions and knowledge sharing
194 among developers of the neuroscience software. We will also use it
195 to update you with summaries of recent relevant developments in
198 * neurodebian-devel_: Technical mailing list for discussions on
199 NeuroDebian development
201 You are welcome also to join #neurodebian IRC room on OFTC network if
202 you have quick questions or want to join a live discussion.
207 We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
208 Italian espresso <coffeeart>`.
210 .. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
212 Thanks to the following institutions and individuals for hosting a mirror:
214 * `Department of Psychological and Brain Sciences at Dartmouth College`_
215 *[us-nh]* (primary mirror)
216 * `Department of Experimental Psychology at the University of Magdeburg`_
218 * `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
219 * `Paul Ivanov`_ *[us-ca]*
220 * `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
222 * `Australia's research and education network (AARNET)
223 <http://www.aarnet.edu.au>`_ *[au]*
224 * Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
225 * Iaroslav Iurchenko *[ua]*
227 If your are interested in mirroring the repository, please see the :ref:`faq`.
229 .. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
230 .. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
231 .. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
232 .. _Paul Ivanov: http://www.pirsquared.org
233 .. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
239 Halchenko, Y.O. & Hanke, M. (2012). `Environments for efficient
240 contemporary research in neuroimaging: PyMVPA and NeuroDebian
241 <_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
242 *Talk given at the University of Pennsylvania School of Medicine*,
243 Philadelphia, PA, USA.
245 Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
246 NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
247 *Talk given at the Max-Planck-Institute for Human Cognitive and Brain
248 Sciences*, Leipzig, Germany.
250 Hanke, M. (2011). `More than batteries included: NeuroDebian
251 <_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
252 *Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,
255 Halchenko, Y. O. (2011). `π's in Debian or Scientific Debian: NumPy, SciPy and beyond
256 <_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
257 *Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
260 Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
261 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
262 *Frontiers in Neuroinformatics, 5:8*.
264 Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
265 platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
266 *Poster presented at the annual meeting of the Organisation for Human Brain
267 Mapping*, Quebec City, Canada.
269 Hanke, M. (2011). `Integrating Condor into the Debian operating system
270 <_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
271 *Talk given at* `CondorWeek 2011
272 <http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
273 Madison, Wisconsin, USA.
275 Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
276 SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
277 Neuroscience*, San Diego, USA.
279 Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
280 (2010). `Having trouble getting your Nature paper? Maybe you are not using the
281 right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster presented at the
282 annual meeting of the Society for Neuroscience*, San Diego, USA.
284 Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
285 neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
286 *Talk given at* DebConf10_, New York City, USA. [video:
287 `low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
288 `high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
290 Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
291 efficiency in cognitive neuroscience research with NeuroDebian
292 <_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
293 meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
295 Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
296 statistical learning, and open-source software to make research more
297 efficient, more open, and more fun
298 <_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
299 `Dartmouth College`_, New Hampshire, USA.
301 .. _DebConf10: http://debconf10.debconf.org/
302 .. _Dartmouth College: http://www.dartmouth.edu/
318 .. probably should be purged altogether
330 .. include:: link_names.txt
331 .. include:: substitutions.txt