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 To enable NeuroDebian on your system, simply copy and paste the following
52 commands into a terminal window:
57 After selecting a release the setup code will be shown here.
60 Once this is done, you have to update the package index and you are ready to
61 install packages. Use your favorite package manager, e.g. synaptic, adept. In
62 the terminal you can use :command:`apt-get`::
65 sudo apt-get install mricron
69 Not every package is available for all distributions/releases. For information
70 about which package version is available for which release and architecture,
71 please have a look at the corresponding package pages.
75 </div> <!-- end reposetup -->
77 <div id="vmsetup" style="display:none">
79 For all non-Debian operating systems the recommended way to deploy NeuroDebian
80 is a `virtual appliance`_. On all modern hardware (built within the last 3-4
81 years) a virtual appliance is a convenient solution to run NeuroDebian
82 simultaneously with the primary operating system -- without noticable
85 1. Install NeuroDebian by first downloading this image file:
89 <div id="vmimagedownload">
90 <a href="http://neuro.debian.net/debian/vm/">NeuroDebian images</a>
93 2. Once downloaded, import this image into your VirtualBox_ installation. If you
94 do not have VirtualBox_ installed yet, visit the `VirtualBox download page
95 <http://www.virtualbox.org/wiki/Downloads>`_ that provides installers for
96 Windows, Linux, Mac and Solaris.
98 3. Please read :ref:`the detailed instructions on setting up the virtual
99 appliance <chap_vm>` to complete the configuration of your NeuroDebian
104 If you still running an older VirtualBox 3.x, download one of the image files
105 listed below. These older releases are distributed as a `zip` file. Please
106 extract all files from the `.zip` file, using appropriate software
107 for your operating system.
109 * `NeuroDebian 6.0.2 image (32bit)
110 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
112 * `NeuroDebian 6.0.2 image (64bit)
113 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
117 </div> <!-- end vmsetup -->
119 .. _virtual appliance: http://en.wikipedia.org/wiki/Virtual_appliance
120 .. _VirtualBox: http://www.virtualbox.org
129 <script src="_static/jquery.livetwitter.min.js"></script>
130 <div id="identica_widget"></div>
131 <script type="text/javascript">
132 $("#identica_widget").liveTwitter('neurodebian',
133 {service: 'identi.ca',
134 mode: 'user_timeline',
139 For more news and information see our :ref:`blog <blog>`. Older news items are
140 available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to
141 subscribe to the NeuroDebian news.
143 .. _identi.ca: http://identi.ca/neurodebian
144 .. _twitter: http://twitter.com/NeuroDebian
154 `Email us directly <team@neuro.debian.net>`_ with any "private"
155 communication. Otherwise please use our public mailing lists, which
156 exist not only to provide user-support but also to establish
157 communication channels within the NeuroDebian community
159 * neurodebian-users_: Discussions and support of NeuroDebian users
161 * neurodebian-upstream_: General discussions and knowledge sharing
162 among developers of neuroscience software. We also use it
163 to update you with summaries of recent relevant developments in
166 * neurodebian-devel_: Technical mailing list for discussions on
167 NeuroDebian development
169 You are welcome also to join #neurodebian IRC room on OFTC network if
170 you have quick questions or want to join a live discussion.
177 `Michael Hanke <http://mih.voxindeserto.de>`_ and `Yaroslav Halchenko
178 <http://www.onerussian.com>`_ originally started NeuroDebian (formerly the
179 `Experimental Psychology Debian packaging project
180 <http://alioth.debian.org/projects/pkg-exppsy>`_) and are the current project
181 leaders. However, the whole project would not be possible without the work of
182 over 3,000 Debian_ developers and contributors who are as enthusiastically
183 building the Debian operating system.
184 A number of packages that are available from the NeuroDebian repository have
185 been contributed by various individuals and other teams in Debian, such as
186 `Debian Med`_ and `Debian Science`_. We want to express our gratitude to all
187 maintainers_ that help to make Debian_ the ultimate software platform for
190 .. _maintainers: pkgs.html#by-maintainer
196 We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
197 Italian espresso <coffeeart>`.
199 .. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
201 Thanks to the following institutions and individuals for hosting a mirror:
203 * `Department of Psychological and Brain Sciences at Dartmouth College`_
204 *[us-nh]* (primary mirror)
205 * `Department of Experimental Psychology at the University of Magdeburg`_
207 * `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
208 * `Paul Ivanov`_ *[us-ca]*
209 * `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
211 * `Australia's research and education network (AARNET)
212 <http://www.aarnet.edu.au>`_ *[au]*
213 * Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
214 * Iaroslav Iurchenko *[ua]*
215 * `Nikolaus Valentin Haenel`_ *[de-v]*
217 If your are interested in mirroring the repository, please see the :ref:`faq`.
219 .. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
220 .. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
221 .. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
222 .. _Paul Ivanov: http://www.pirsquared.org
223 .. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
224 .. _Nikolaus Valentin Haenel: http://haenel.co
230 Hanke, M. (2012). `Share your tools! But fear the wombat! Seriously.
231 <http://neuro.debian.net/_files/Hanke_FearTheWombat_Brainhack2012.pdf>`_ *Talk
232 given at* `Brainhack <http://brainhack.org/2012/04/06/brainhack-2012-unconference>`_ 2012 at the
233 Max-Planck-Institute for Human Cognitive and Brain Sciences*, Leipzig, Germany.
234 [`video <http://youtu.be/8t6znEOEDVo>`_]
236 Hanke, M. (2012). `Computational and cognitive neuroscience boosted by Debian
237 OR Just using Debian is not enough
238 <http://neuro.debian.net/_files/Hanke_UsingDebianIsNotEnough_ESRF2012.pdf>`_.
239 Talk given at the workshop "Debian for Scientific Facilities Days" at the
240 European Synchrotron Radiation Facility (ESRF), Grenoble, France.
242 Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
243 next step: An integrated, community-driven computing platform for neuroscience
244 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_. *Frontiers in Neuroinformatics*,
249 <span id="morepublicationsbutton" class="button" title="Click to toogle more"></span>
250 <div id="morepublications">
252 Hanke, M. (2012). `The why and how of getting packaged
253 <_files/Hanke_GetPackaged_CodeJam5_2012.pdf>`_.
254 *Talk given at BrainScaleS CodeJam 5, Convergence in Computational Neuroscience*,
255 University of Edinburgh, Edinburgh, UK.
257 Halchenko, Y. O. & Hanke, M. (2012). `Environments for efficient
258 contemporary research in neuroimaging: PyMVPA and NeuroDebian
259 <_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
260 *Talk given at the University of Pennsylvania School of Medicine*,
261 Philadelphia, PA, USA.
263 Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
264 NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
265 *Talk given at the Max-Planck-Institute for Human Cognitive and Brain
266 Sciences*, Leipzig, Germany.
268 Hanke, M. (2011). `More than batteries included: NeuroDebian
269 <_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
270 *Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,
273 Halchenko, Y. O. (2011). `π's in Debian or Scientific Debian: NumPy, SciPy and beyond
274 <_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
275 *Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
278 Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
279 <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
280 *Frontiers in Neuroinformatics, 5:8*.
282 Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
283 platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
284 *Poster presented at the annual meeting of the Organisation for Human Brain
285 Mapping*, Quebec City, Canada.
287 Hanke, M. (2011). `Integrating Condor into the Debian operating system
288 <_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
289 *Talk given at* `CondorWeek 2011
290 <http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
291 Madison, Wisconsin, USA.
293 Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
294 SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
295 Neuroscience*, San Diego, USA.
297 Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
298 (2010). `Having trouble getting your Nature paper? Maybe you are not using the
299 right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster presented at the
300 annual meeting of the Society for Neuroscience*, San Diego, USA.
302 Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
303 neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
304 *Talk given at* DebConf10_, New York City, USA. [video:
305 `low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
306 `high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
308 Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
309 efficiency in cognitive neuroscience research with NeuroDebian
310 <_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
311 meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
313 Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
314 statistical learning, and open-source software to make research more
315 efficient, more open, and more fun
316 <_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
317 `Dartmouth College`_, New Hampshire, USA.
323 .. _DebConf10: http://debconf10.debconf.org/
324 .. _Dartmouth College: http://www.dartmouth.edu/
331 <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>
336 We encourage you to participate in the `popularity
337 contest <http://popcon.debian.org>`_ (popcon), which anonymously
338 collects the list of packages you installed/use on your system.
339 Collecting such statistics is of particular importance for research
340 software projects as a prove of an existing user-base. If upon
341 installation of the system you rejected the invitation to participate
342 you can always change your decision by running::
344 sudo dpkg-reconfigure popularity-contest
348 If you are deploying multiple systems through cloning, to not have
349 all systems considered as one, it would be necessary to re-generate
350 the random MY_HOSTID. Following commands ran as root should do it
351 (as root) without any interactive dialog::
353 sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
354 DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
356 In addition to popcon pages for your "core" distribution (e.g. `Debian
357 <http://popcon.debian.org/>`__ or `Ubuntu
358 <http://popcon.ubuntu.com/>`__) you can see/get statistics for
359 submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
360 know that you are already contributing back to the community.
377 .. probably should be purged altogether
389 .. include:: link_names.txt
390 .. include:: substitutions.txt
394 <script type="text/javascript">
395 $(document).ready(function($) {
396 setInterval(function(){
397 $.get('testimonials.html', function(data) {
398 var quotes = $("blockquote", data);
399 var idx = Math.floor(quotes.length * Math.random());
400 $('#randomquote').html(quotes[idx]);
401 }); // update callback
402 }, 60000); // set interval
404 //$("h1").html("NeuroDebian <span style=\"font-size:14px\">— the ultimate neuroscience software platform</span>")
406 function foldbuttontoggle(foldname) {
407 var foldid = '#' + foldname;
408 var buttonid = foldid + 'button';
409 $(buttonid).on('click', function() {
410 $('#' + foldname).slideToggle();
411 if ($(buttonid).html() == "↓↓↓") {
412 $(buttonid).html("↑↑↑");
415 $(buttonid).html("↓↓↓");
419 $(buttonid).html("↓↓↓");
422 function createvmdownload(rel, mir) {
423 var img_version = '6.0.5';
428 if (rel == 'win32') {
431 img_suffix = 'amd64';
434 base_url = mirrors[mir] + '/vm/';
435 img_url = base_url + 'NeuroDebian_' + img_version + '_' + img_suffix + '.ova';
436 md5sum_url = base_url + 'MD5SUMS';
438 return 'Internal error';
440 return '<blockquote><a href="' + img_url
441 + '">Virtual applicance image</a> [<a title="Verify image integrity by dowloading this file and running `md5sum -c MD5SUMS`" href="'
443 + '">MD5SUM</a>, <a title="Verify authenticity of the MD5SUM file by downloading this file and running `gpg –verify MD5SUMS.gpg`" href="'
444 + md5sum_url + '.gpg">MD5SUM.gpg</a>]</blockquote>' ;
448 function createrepourl(rel, mir) {
449 if(rel in rel2name && mir in mirrors) {
451 var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel2name[rel] + "."
452 + mir + " | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n"
453 + "sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9\n";
458 function updateout(rel, mir) {
459 if (rel != '' && mir != '') {
460 if (rel in {'win32':'', 'win64':'', 'mac':''}) {
461 $('#vmimagedownload').html(createvmdownload(rel, mir));
462 $('#vmsetup').slideDown();
463 $('#reposetup').slideUp();
465 $('#code').text(createrepourl(rel, mir));
466 $('#reposetup').slideDown();
467 $('#vmsetup').slideUp();
472 $('#reposetup').slideUp();
473 $('#vmsetup').slideUp();
476 $('#release').change(function() {
477 var singleValues = $("#release").val();
478 var mirrorVal = $("#mirror").val();
479 updateout(singleValues, mirrorVal);
481 $('#mirror').change(function() {
482 var singleValues = $("#release").val();
483 var mirrorVal = $("#mirror").val();
484 updateout(singleValues, mirrorVal);
487 $(document).ready(function($) {
488 updateout($("#release").val(), $("#mirror").val());
491 foldbuttontoggle('morepublications');