3 ***************************************************
4 Welcome to the Ultimate Platform for Neuroscience
5 ***************************************************
10 NeuroDebian provides a turnkey software platform for neuroscience
11 that is created by integrating research tools with the Debian_ operating
12 system. If you are using such software on Debian_ or its derivatives,
13 such as Ubuntu_, chances are that you are already using NeuroDebian.
15 This website provides a :ref:`supplementary repository <repository_howto>` with
16 both unofficial or prospective packages which are not (yet) available from the
17 main Debian_ archive, as well as backported or simply rebuilt latest versions
18 of software. NeuroDebian serves as an "upstream" to some :ref:`derivative
19 <chap_derivatives>` projects. Please see the :ref:`faq` for more information
20 about the goals of this project, and :ref:`read what people say about it
21 <testimonials>`. Take a look at the :ref:`list of our current and planned
22 projects <projects>` if you want to get involved. This service is provided "as
23 is". There is no guarantee that a package works as expected, so use them at
24 your own risk. If you encounter problems, please `report <#contacts>`_ them.
25 Please help us |spread|:
27 Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
28 next step: An integrated, community-driven computing platform for neuroscience
29 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_.
30 *Frontiers in Neuroinformatics*, 6:22.
35 <a href="pkgs.html"><img border="0" src="_static/package.png" title="Software package list" /></a>
36 <a href="pkglists/pkgs-by_release-datasets_(data).html"><img border="0" src="_static/datasets.png" title="Dataset package list" /></a>
37 <a href="vm.html"><img border="0" src="_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /></a>
38 <a href="debian/pool"><img border="0" src="_static/pool.png" title="Go to the package pool (deep and cold, only for experts)" /></a>
39 <a href="projects.html"><img border="0" src="_static/workarea.png" title="Current and planned projects: Get involved!" /></a>
40 <a href="derivatives.html"><img border="0" src="_static/derivatives.png" title="NeuroDebian Derivatives" /></a>
41 <a href="blog/index.html"><img border="0" src="_static/rssfeeds.png" title="NeuroDebian Insider Blog" /></a>
44 .. _Ubuntu: http://www.ubuntu.com
53 <script src="_static/jquery.livetwitter.min.js"></script>
54 <div id="identica_widget"></div>
55 <script type="text/javascript">
56 $("#identica_widget").liveTwitter('neurodebian',
57 {service: 'identi.ca',
58 mode: 'user_timeline',
63 For more news and information see our :ref:`blog <blog>`. Older news items are
64 available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to
65 subscribe to the NeuroDebian news.
67 .. _identi.ca: http://identi.ca/neurodebian
68 .. _twitter: http://twitter.com/NeuroDebian
74 How to use this repository
75 ==========================
77 To enable the NeuroDebian repository on your system, select your Debian or
78 Ubuntu release and a repository mirror from the lists below. Upon selection
79 a short command snippet will be displayed that can be copied and pasted into
80 a terminal session. These commands will configure the system package manager
81 with the NeuroDebian repository key and package source information.
83 .. include:: sources_lists
85 Once this is done, you have to update the package index and you are ready to
86 install packages. Use your favorite package manager, e.g. synaptic, adept. In
87 the terminal you can use :command:`apt-get`::
90 sudo apt-get install mricron
94 Not every package is available for all distributions/releases. For information
95 about which package version is available for which release and architecture,
96 please have a look at the corresponding package pages.
100 <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>
105 We encourage you to participate in the `popularity
106 contest <http://popcon.debian.org>`_ (popcon), which anonymously
107 collects the list of packages you installed/use on your system.
108 Collecting such statistics is of particular importance for research
109 software projects as a prove of an existing user-base. If upon
110 installation of the system you rejected the invitation to participate
111 you can always change your decision by running::
113 sudo dpkg-reconfigure popularity-contest
117 If you are deploying multiple systems through cloning, to not have
118 all systems considered as one, it would be necessary to re-generate
119 the random MY_HOSTID. Following commands ran as root should do it
120 (as root) without any interactive dialog::
122 sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
123 DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
125 In addition to popcon pages for your "core" distribution (e.g. `Debian
126 <http://popcon.debian.org/>`__ or `Ubuntu
127 <http://popcon.ubuntu.com/>`__) you can see/get statistics for
128 submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
129 know that you are already contributing back to the community.
131 .. _chap_installation:
133 Ways to use NeuroDebian
134 =======================
139 If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
140 provided as a convenient testing and evaluation environment. After a few
141 simple steps to setup the virtual machine, you will be able to use NeuroDebian_
142 as an integral part of your existing working environment without any sacrifice.
143 The virtual machine is also a suitable environment to temporarily deploy
144 neuroscience software on machines running other operating systems, e.g. for the
145 purpose of teaching a neuroimaging data analysis course in a multipurpose
152 Having been exposed to the wonders of NeuroDebian_ you are no longer
153 satisfied with your previous choice of operating system? We would
154 recommend installing Debian_ to replace or complement (dual-boot) your
155 existing OS. Please visit `"Getting Debian"
156 <http://www.debian.org/distrib/>`_ to obtain the images for your
157 hardware architecture and then simply add |repos|.
166 `Michael Hanke <http://mih.voxindeserto.de>`_ and `Yaroslav Halchenko
167 <http://www.onerussian.com>`_ originally started NeuroDebian (formerly the
168 `Experimental Psychology Debian packaging project
169 <http://alioth.debian.org/projects/pkg-exppsy>`_) and are the current project
170 leaders. However, the whole project would not be possible without the work of
171 over 3,000 Debian_ developers and contributors who are as enthusiastically
172 building the Debian operating system.
173 A number of packages that are available from the NeuroDebian repository have
174 been contributed by various individuals and other teams in Debian, such as
175 `Debian Med`_ and `Debian Science`_. We want to express our gratitude to all
176 maintainers_ that help to make Debian_ the ultimate software platform for
179 .. _maintainers: pkgs.html#by-maintainer
187 `Email us directly <team@neuro.debian.net>`_ with any "private"
188 communication. Otherwise please use our public mailing lists, which
189 exist not only to provide user-support but also to establish
190 communication channels within the NeuroDebian community
192 * neurodebian-users_: Discussions and support of NeuroDebian users
194 * neurodebian-upstream_: General discussions and knowledge sharing
195 among developers of neuroscience software. We also use it
196 to update you with summaries of recent relevant developments in
199 * neurodebian-devel_: Technical mailing list for discussions on
200 NeuroDebian development
202 You are welcome also to join #neurodebian IRC room on OFTC network if
203 you have quick questions or want to join a live discussion.
208 We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
209 Italian espresso <coffeeart>`.
211 .. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
213 Thanks to the following institutions and individuals for hosting a mirror:
215 * `Department of Psychological and Brain Sciences at Dartmouth College`_
216 *[us-nh]* (primary mirror)
217 * `Department of Experimental Psychology at the University of Magdeburg`_
219 * `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
220 * `Paul Ivanov`_ *[us-ca]*
221 * `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
223 * `Australia's research and education network (AARNET)
224 <http://www.aarnet.edu.au>`_ *[au]*
225 * Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
226 * Iaroslav Iurchenko *[ua]*
228 If your are interested in mirroring the repository, please see the :ref:`faq`.
230 .. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
231 .. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
232 .. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
233 .. _Paul Ivanov: http://www.pirsquared.org
234 .. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
240 Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
241 next step: An integrated, community-driven computing platform for neuroscience
242 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_. *Frontiers in Neuroinformatics*,
245 Hanke, M. (2012). `The why and how of getting packaged
246 <_files/Hanke_GetPackaged_CodeJam5_2012.pdf>`_.
247 *Talk given at BrainScaleS CodeJam 5, Convergence in Computational Neuroscience*,
248 University of Edinburgh, Edinburgh, UK.
250 Halchenko, Y. O. & Hanke, M. (2012). `Environments for efficient
251 contemporary research in neuroimaging: PyMVPA and NeuroDebian
252 <_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
253 *Talk given at the University of Pennsylvania School of Medicine*,
254 Philadelphia, PA, USA.
256 Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
257 NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
258 *Talk given at the Max-Planck-Institute for Human Cognitive and Brain
259 Sciences*, Leipzig, Germany.
261 Hanke, M. (2011). `More than batteries included: NeuroDebian
262 <_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
263 *Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,
266 Halchenko, Y. O. (2011). `π's in Debian or Scientific Debian: NumPy, SciPy and beyond
267 <_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
268 *Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
271 Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
272 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
273 *Frontiers in Neuroinformatics, 5:8*.
275 Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
276 platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
277 *Poster presented at the annual meeting of the Organisation for Human Brain
278 Mapping*, Quebec City, Canada.
280 Hanke, M. (2011). `Integrating Condor into the Debian operating system
281 <_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
282 *Talk given at* `CondorWeek 2011
283 <http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
284 Madison, Wisconsin, USA.
286 Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
287 SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
288 Neuroscience*, San Diego, USA.
290 Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
291 (2010). `Having trouble getting your Nature paper? Maybe you are not using the
292 right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster presented at the
293 annual meeting of the Society for Neuroscience*, San Diego, USA.
295 Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
296 neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
297 *Talk given at* DebConf10_, New York City, USA. [video:
298 `low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
299 `high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
301 Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
302 efficiency in cognitive neuroscience research with NeuroDebian
303 <_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
304 meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
306 Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
307 statistical learning, and open-source software to make research more
308 efficient, more open, and more fun
309 <_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
310 `Dartmouth College`_, New Hampshire, USA.
312 .. _DebConf10: http://debconf10.debconf.org/
313 .. _Dartmouth College: http://www.dartmouth.edu/
330 .. probably should be purged altogether
342 .. include:: link_names.txt
343 .. include:: substitutions.txt