7 NeuroDebian provides a large collection of popular neuroscience research
8 software for the Debian_ operating system as well as Ubuntu_ and other
9 derivatives. Popular packages include FSL, Freesurfer, AFNI, PyMVPA and
10 :ref:`many others <pkglists>`. While we do strive to maintain a high level of
11 quality, we make no guarantee that a given package works as expected, so use
12 them at your own risk. If you do encounter problems or would just like to thank
13 us, simply `send us an email <#contacts>`_.
15 Learn more about NeuroDebian, the goals of this project, and help us |spread|!
17 Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
18 next step: An integrated, community-driven computing platform for neuroscience
19 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_.
20 *Frontiers in Neuroinformatics*, 6:22.
24 <!-- for dynamic quote update via javascript -->
26 <div id="randomquote" title="Feedback from the community">
33 </div><!-- randomquote -->
35 .. _Ubuntu: http://www.ubuntu.com
38 .. _chap_installation:
43 Make your selection to enable NeuroDebian on your computer:
45 .. include:: sources_lists
49 <div id="reposetup" style="display:none">
51 <p>Copy and paste the following command into a terminal window:</p>
53 After selecting a release the setup code will be shown here.
56 Once this is done, you have to update the package index and you are ready to
57 install packages. Use your favorite package manager, e.g. synaptic, adept. In
58 the terminal you can use :command:`apt-get`::
61 sudo apt-get install mricron
65 Not every package is available for all distributions/releases. For information
66 about which package version is available for which release and architecture,
67 please have a look at the corresponding package pages.
71 </div> <!-- end reposetup -->
73 <div id="vmsetup" style="display:none">
75 If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
76 provided as a convenient testing and evaluation environment. After a few
77 simple steps to setup the virtual machine, you will be able to use NeuroDebian_
78 as an integral part of your existing working environment without any sacrifice.
79 The virtual machine is also a suitable environment to temporarily deploy
80 neuroscience software on machines running other operating systems, e.g. for the
81 purpose of teaching a neuroimaging data analysis course in a multipurpose
88 Having been exposed to the wonders of NeuroDebian_ you are no longer
89 satisfied with your previous choice of operating system? We would
90 recommend installing Debian_ to replace or complement (dual-boot) your
91 existing OS. Please visit `"Getting Debian"
92 <http://www.debian.org/distrib/>`_ to obtain the images for your
93 hardware architecture and then simply add |repos|.
97 </div> <!-- end vmsetup -->
106 <script src="_static/jquery.livetwitter.min.js"></script>
107 <div id="identica_widget"></div>
108 <script type="text/javascript">
109 $("#identica_widget").liveTwitter('neurodebian',
110 {service: 'identi.ca',
111 mode: 'user_timeline',
116 For more news and information see our :ref:`blog <blog>`. Older news items are
117 available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to
118 subscribe to the NeuroDebian news.
120 .. _identi.ca: http://identi.ca/neurodebian
121 .. _twitter: http://twitter.com/NeuroDebian
131 `Email us directly <team@neuro.debian.net>`_ with any "private"
132 communication. Otherwise please use our public mailing lists, which
133 exist not only to provide user-support but also to establish
134 communication channels within the NeuroDebian community
136 * neurodebian-users_: Discussions and support of NeuroDebian users
138 * neurodebian-upstream_: General discussions and knowledge sharing
139 among developers of neuroscience software. We also use it
140 to update you with summaries of recent relevant developments in
143 * neurodebian-devel_: Technical mailing list for discussions on
144 NeuroDebian development
146 You are welcome also to join #neurodebian IRC room on OFTC network if
147 you have quick questions or want to join a live discussion.
154 `Michael Hanke <http://mih.voxindeserto.de>`_ and `Yaroslav Halchenko
155 <http://www.onerussian.com>`_ originally started NeuroDebian (formerly the
156 `Experimental Psychology Debian packaging project
157 <http://alioth.debian.org/projects/pkg-exppsy>`_) and are the current project
158 leaders. However, the whole project would not be possible without the work of
159 over 3,000 Debian_ developers and contributors who are as enthusiastically
160 building the Debian operating system.
161 A number of packages that are available from the NeuroDebian repository have
162 been contributed by various individuals and other teams in Debian, such as
163 `Debian Med`_ and `Debian Science`_. We want to express our gratitude to all
164 maintainers_ that help to make Debian_ the ultimate software platform for
167 .. _maintainers: pkgs.html#by-maintainer
173 We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
174 Italian espresso <coffeeart>`.
176 .. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
178 Thanks to the following institutions and individuals for hosting a mirror:
180 * `Department of Psychological and Brain Sciences at Dartmouth College`_
181 *[us-nh]* (primary mirror)
182 * `Department of Experimental Psychology at the University of Magdeburg`_
184 * `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
185 * `Paul Ivanov`_ *[us-ca]*
186 * `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
188 * `Australia's research and education network (AARNET)
189 <http://www.aarnet.edu.au>`_ *[au]*
190 * Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
191 * Iaroslav Iurchenko *[ua]*
192 * `Nikolaus Valentin Haenel`_ *[de-v]*
194 If your are interested in mirroring the repository, please see the :ref:`faq`.
196 .. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
197 .. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
198 .. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
199 .. _Paul Ivanov: http://www.pirsquared.org
200 .. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
201 .. _Nikolaus Valentin Haenel: http://haenel.co
207 Hanke, M. (2012). `Share your tools! But fear the wombat! Seriously.
208 <http://neuro.debian.net/_files/Hanke_FearTheWombat_Brainhack2012.pdf>`_ *Talk
209 given at* `Brainhack <http://brainhack.org/2012/04/06/brainhack-2012-unconference>`_ 2012 at the
210 Max-Planck-Institute for Human Cognitive and Brain Sciences*, Leipzig, Germany.
211 [`video <http://youtu.be/8t6znEOEDVo>`_]
213 Hanke, M. (2012). `Computational and cognitive neuroscience boosted by Debian
214 OR Just using Debian is not enough
215 <http://neuro.debian.net/_files/Hanke_UsingDebianIsNotEnough_ESRF2012.pdf>`_.
216 Talk given at the workshop "Debian for Scientific Facilities Days" at the
217 European Synchrotron Radiation Facility (ESRF), Grenoble, France.
219 Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
220 next step: An integrated, community-driven computing platform for neuroscience
221 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_. *Frontiers in Neuroinformatics*,
226 <span id="morepublicationsbutton" class="button" title="Click to toogle more"></span>
227 <div id="morepublications">
229 Hanke, M. (2012). `The why and how of getting packaged
230 <_files/Hanke_GetPackaged_CodeJam5_2012.pdf>`_.
231 *Talk given at BrainScaleS CodeJam 5, Convergence in Computational Neuroscience*,
232 University of Edinburgh, Edinburgh, UK.
234 Halchenko, Y. O. & Hanke, M. (2012). `Environments for efficient
235 contemporary research in neuroimaging: PyMVPA and NeuroDebian
236 <_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
237 *Talk given at the University of Pennsylvania School of Medicine*,
238 Philadelphia, PA, USA.
240 Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
241 NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
242 *Talk given at the Max-Planck-Institute for Human Cognitive and Brain
243 Sciences*, Leipzig, Germany.
245 Hanke, M. (2011). `More than batteries included: NeuroDebian
246 <_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
247 *Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,
250 Halchenko, Y. O. (2011). `π's in Debian or Scientific Debian: NumPy, SciPy and beyond
251 <_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
252 *Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
255 Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
256 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
257 *Frontiers in Neuroinformatics, 5:8*.
259 Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
260 platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
261 *Poster presented at the annual meeting of the Organisation for Human Brain
262 Mapping*, Quebec City, Canada.
264 Hanke, M. (2011). `Integrating Condor into the Debian operating system
265 <_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
266 *Talk given at* `CondorWeek 2011
267 <http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
268 Madison, Wisconsin, USA.
270 Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
271 SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
272 Neuroscience*, San Diego, USA.
274 Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
275 (2010). `Having trouble getting your Nature paper? Maybe you are not using the
276 right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster presented at the
277 annual meeting of the Society for Neuroscience*, San Diego, USA.
279 Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
280 neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
281 *Talk given at* DebConf10_, New York City, USA. [video:
282 `low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
283 `high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
285 Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
286 efficiency in cognitive neuroscience research with NeuroDebian
287 <_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
288 meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
290 Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
291 statistical learning, and open-source software to make research more
292 efficient, more open, and more fun
293 <_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
294 `Dartmouth College`_, New Hampshire, USA.
300 .. _DebConf10: http://debconf10.debconf.org/
301 .. _Dartmouth College: http://www.dartmouth.edu/
308 <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>
313 We encourage you to participate in the `popularity
314 contest <http://popcon.debian.org>`_ (popcon), which anonymously
315 collects the list of packages you installed/use on your system.
316 Collecting such statistics is of particular importance for research
317 software projects as a prove of an existing user-base. If upon
318 installation of the system you rejected the invitation to participate
319 you can always change your decision by running::
321 sudo dpkg-reconfigure popularity-contest
325 If you are deploying multiple systems through cloning, to not have
326 all systems considered as one, it would be necessary to re-generate
327 the random MY_HOSTID. Following commands ran as root should do it
328 (as root) without any interactive dialog::
330 sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
331 DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
333 In addition to popcon pages for your "core" distribution (e.g. `Debian
334 <http://popcon.debian.org/>`__ or `Ubuntu
335 <http://popcon.ubuntu.com/>`__) you can see/get statistics for
336 submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
337 know that you are already contributing back to the community.
354 .. probably should be purged altogether
366 .. include:: link_names.txt
367 .. include:: substitutions.txt
371 <script type="text/javascript">
372 $(document).ready(function($) {
373 setInterval(function(){
374 $.get('testimonials.html', function(data) {
375 var quotes = $("blockquote", data);
376 var idx = Math.floor(quotes.length * Math.random());
377 $('#randomquote').html(quotes[idx]);
378 }); // update callback
379 }, 60000); // set interval
381 //$("h1").html("NeuroDebian <span style=\"font-size:14px\">— the ultimate neuroscience software platform</span>")
383 function foldbuttontoggle(foldname) {
384 var foldid = '#' + foldname;
385 var buttonid = foldid + 'button';
386 $(buttonid).on('click', function() {
387 $('#' + foldname).slideToggle();
388 if ($(buttonid).html() == "↓↓↓") {
389 $(buttonid).html("↑↑↑");
392 $(buttonid).html("↓↓↓");
396 $(buttonid).html("↓↓↓");
399 function createrepourl(rel, mir) {
400 if(rel in rel2name && mir in mirrors) {
402 var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel2name[rel] + "."
403 + mir + " | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n"
404 + "sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9\n";
409 function updateout(rel, mir) {
410 if (rel != '' && mir != '') {
411 $('#code').text(createrepourl(rel, mir));
412 if (rel in {'win':'', 'rel':''}) {
413 $('#vmsetup').slideDown();
414 $('#reposetup').slideUp();
416 $('#reposetup').slideDown();
417 $('#vmsetup').slideUp();
422 $('#reposetup').slideUp();
423 $('#vmsetup').slideUp();
426 $('#release').change(function() {
427 var singleValues = $("#release").val();
428 var mirrorVal = $("#mirror").val();
429 updateout(singleValues, mirrorVal);
431 $('#mirror').change(function() {
432 var singleValues = $("#release").val();
433 var mirrorVal = $("#mirror").val();
434 updateout(singleValues, mirrorVal);
438 foldbuttontoggle('morepublications');