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="blog/index.html"><img border="0" src="_static/rssfeeds.png" title="NeuroDebian Insider Blog" /></a>
42 .. _Ubuntu: http://www.ubuntu.com
51 <script src="_static/jquery.livetwitter.min.js"></script>
52 <div id="identica_widget"></div>
53 <script type="text/javascript">
54 $("#identica_widget").liveTwitter('neurodebian',
55 {service: 'identi.ca',
56 mode: 'user_timeline',
61 For more news and information see our :ref:`blog <blog>`. Older news items are
62 available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to
63 subscribe to the NeuroDebian news.
65 .. _identi.ca: http://identi.ca/neurodebian
66 .. _twitter: http://twitter.com/NeuroDebian
72 How to use this repository
73 ==========================
75 To enable the NeuroDebian repository on your system, select your Debian or
76 Ubuntu release and a repository mirror from the lists below. Upon selection
77 a short command snippet will be displayed that can be copied and pasted into
78 a terminal session. These commands will configure the system package manager
79 with the NeuroDebian repository key and package source information.
81 .. include:: sources_lists
83 Once this is done, you have to update the package index and you are ready to
84 install packages. Use your favorite package manager, e.g. synaptic, adept. In
85 the terminal you can use :command:`apt-get`::
88 sudo apt-get install mricron
92 Not every package is available for all distributions/releases. For information
93 about which package version is available for which release and architecture,
94 please have a look at the corresponding package pages.
98 <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>
103 We encourage you to participate in the `popularity
104 contest <http://popcon.debian.org>`_ (popcon), which anonymously
105 collects the list of packages you installed/use on your system.
106 Collecting such statistics is of particular importance for research
107 software projects as a prove of an existing user-base. If upon
108 installation of the system you rejected the invitation to participate
109 you can always change your decision by running::
111 sudo dpkg-reconfigure popularity-contest
115 If you are deploying multiple systems through cloning, to not have
116 all systems considered as one, it would be necessary to re-generate
117 the random MY_HOSTID. Following commands ran as root should do it
118 (as root) without any interactive dialog::
120 sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
121 DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
123 In addition to popcon pages for your "core" distribution (e.g. `Debian
124 <http://popcon.debian.org/>`__ or `Ubuntu
125 <http://popcon.ubuntu.com/>`__) you can see/get statistics for
126 submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
127 know that you are already contributing back to the community.
129 .. _chap_installation:
131 Ways to use NeuroDebian
132 =======================
137 If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
138 provided as a convenient testing and evaluation environment. After a few
139 simple steps to setup the virtual machine, you will be able to use NeuroDebian_
140 as an integral part of your existing working environment without any sacrifice.
141 The virtual machine is also a suitable environment to temporarily deploy
142 neuroscience software on machines running other operating systems, e.g. for the
143 purpose of teaching a neuroimaging data analysis course in a multipurpose
150 Having been exposed to the wonders of NeuroDebian_ you are no longer
151 satisfied with your previous choice of operating system? We would
152 recommend installing Debian_ to replace or complement (dual-boot) your
153 existing OS. Please visit `"Getting Debian"
154 <http://www.debian.org/distrib/>`_ to obtain the images for your
155 hardware architecture and then simply add |repos|.
164 Our main goal is to provide neuroscience FOSS_ for Debian_. Thus the
165 whole project would not be possible without the work of over 3,000
166 Debian_ developers and contributors who are as enthusiastically pursuing
167 a similar goal. To add our share -- Debian_ packages of FOSS_ for
168 neuroscience research -- the `Experimental Psychology Debian packaging
169 project <http://alioth.debian.org/projects/pkg-exppsy>`_ was created
170 to formally join the forces of
172 * `Michael Hanke <http://mih.voxindeserto.de>`_
173 * `Yaroslav Halchenko <http://www.onerussian.com>`_
175 A number of packages that are now available from the NeuroDebian repository
176 were not packaged by our team, but similar Debian teams. Therefore we want to
177 express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
185 `Email us directly <team@neuro.debian.net>`_ with any "private"
186 communication. Otherwise please use our public mailing lists, which
187 exist not only to provide user-support but also to establish
188 communication channels within the NeuroDebian community
190 * neurodebian-users_: Discussions and support of NeuroDebian users
192 * neurodebian-upstream_: General discussions and knowledge sharing
193 among developers of the neuroscience software. We will also use it
194 to update you with summaries of recent relevant developments in
197 * neurodebian-devel_: Technical mailing list for discussions on
198 NeuroDebian development
200 You are welcome also to join #neurodebian IRC room on OFTC network if
201 you have quick questions or want to join a live discussion.
206 We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
207 Italian espresso <coffeeart>`.
209 .. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
211 Thanks to the following institutions and individuals for hosting a mirror:
213 * `Department of Psychological and Brain Sciences at Dartmouth College`_
214 *[us-nh]* (primary mirror)
215 * `Department of Experimental Psychology at the University of Magdeburg`_
217 * `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
218 * `Paul Ivanov`_ *[us-ca]*
219 * `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
221 * `Australia's research and education network (AARNET)
222 <http://www.aarnet.edu.au>`_ *[au]*
223 * Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
225 If your are interested in mirroring the repository, please see the :ref:`faq`.
227 .. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
228 .. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
229 .. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
230 .. _Paul Ivanov: http://www.pirsquared.org
231 .. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
237 Halchenko, Y.O. & Hanke, M. (2012). `Environments for efficient
238 contemporary research in neuroimaging: PyMVPA and NeuroDebian
239 <_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
240 *Talk given at the University of Pennsylvania School of Medicine*,
241 Philadelphia, PA, USA.
243 Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
244 NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
245 *Talk given at the Max-Planck-Institute for Human Cognitive and Brain
246 Sciences*, Leipzig, Germany.
248 Hanke, M. (2011). `More than batteries included: NeuroDebian
249 <_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
250 *Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,
253 Halchenko, Y. O. (2011). `π's in Debian or Scientific Debian: NumPy, SciPy and beyond
254 <_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
255 *Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
258 Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
259 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
260 *Frontiers in Neuroinformatics, 5:8*.
262 Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
263 platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
264 *Poster presented at the annual meeting of the Organisation for Human Brain
265 Mapping*, Quebec City, Canada.
267 Hanke, M. (2011). `Integrating Condor into the Debian operating system
268 <_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
269 *Talk given at* `CondorWeek 2011
270 <http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
271 Madison, Wisconsin, USA.
273 Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
274 SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
275 Neuroscience*, San Diego, USA.
277 Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
278 (2010). `Having trouble getting your Nature paper? Maybe you are not using the
279 right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster presented at the
280 annual meeting of the Society for Neuroscience*, San Diego, USA.
282 Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
283 neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
284 *Talk given at* DebConf10_, New York City, USA. [video:
285 `low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
286 `high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
288 Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
289 efficiency in cognitive neuroscience research with NeuroDebian
290 <_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
291 meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
293 Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
294 statistical learning, and open-source software to make research more
295 efficient, more open, and more fun
296 <_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
297 `Dartmouth College`_, New Hampshire, USA.
299 .. _DebConf10: http://debconf10.debconf.org/
300 .. _Dartmouth College: http://www.dartmouth.edu/
316 .. probably should be purged altogether
328 .. include:: link_names.txt
329 .. include:: substitutions.txt