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 <div class="linkmore"><a href="/publications.html">more publications</a></div>
25 <div class="clearer"></div>
26 <!-- for dynamic quote update via javascript -->
28 <div id="randomquote" title="Feedback from the community">
35 </div><!-- randomquote -->
36 <div class="linkmore"><a href="/testimonials.html">more testimonials</a></div>
38 .. _Ubuntu: http://www.ubuntu.com
41 .. _chap_installation:
46 Choose on which operating system you want to run NeuroDebian, and select a
47 download server close to you:
49 .. include:: sources_lists
53 <div id="reposetup" style="display:none">
55 To enable NeuroDebian on your system, simply copy and paste the following
56 commands into a terminal window:
61 After selecting a release the setup code will be shown here.
64 Once this is done, you have to update the package index and you are ready to
65 install packages. Use your favorite package manager, e.g. synaptic, adept. In
66 the terminal you can use :command:`apt-get`::
69 sudo apt-get install mricron
73 Not every package is available for all distributions/releases. For information
74 about which package version is available for which release and architecture,
75 please have a look at the corresponding package pages.
79 </div> <!-- end reposetup -->
81 <div id="vmsetup" style="display:none">
83 For all non-Debian operating systems the recommended way to deploy NeuroDebian
84 is a `virtual appliance`_. On all modern hardware (built within the last 3-4
85 years) a virtual appliance is a convenient solution to run NeuroDebian
86 simultaneously with the primary operating system -- without noticable
89 1. Install NeuroDebian by first downloading this image file:
93 <div id="vmimagedownload">
94 <a href="http://neuro.debian.net/debian/vm/">NeuroDebian images</a>
97 2. Once downloaded, import this image into your VirtualBox_ installation. If you
98 do not have VirtualBox_ installed yet, visit the `VirtualBox download page
99 <http://www.virtualbox.org/wiki/Downloads>`_ that provides installers for
100 Windows, Linux, Mac and Solaris.
102 3. Please read :ref:`the detailed instructions on setting up the virtual
103 appliance <chap_vm>` to complete the configuration of your NeuroDebian
108 If you still running an older VirtualBox 3.x, download one of the image files
109 listed below. These older releases are distributed as a `zip` file. Please
110 extract all files from the `.zip` file, using appropriate software
111 for your operating system.
113 * `NeuroDebian 6.0.2 image (32bit)
114 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
116 * `NeuroDebian 6.0.2 image (64bit)
117 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
121 </div> <!-- end vmsetup -->
123 .. _virtual appliance: http://en.wikipedia.org/wiki/Virtual_appliance
124 .. _VirtualBox: http://www.virtualbox.org
133 <script src="_static/jquery.livetwitter.min.js"></script>
134 <div id="identica_widget"></div>
135 <script type="text/javascript">
136 $("#identica_widget").liveTwitter('neurodebian',
137 {service: 'identi.ca',
138 mode: 'user_timeline',
143 .. _identi.ca: http://identi.ca/neurodebian
144 .. _twitter: http://twitter.com/NeuroDebian
153 * :ref:`Team <chap_team>`
154 * :ref:`chap_popularity`
157 * :ref:`chap_publications`
158 * :ref:`testimonials`
164 * :ref:`Software <pkglists>`
165 * :ref:`Data <pkgs-by_purpose-neuroscience_datasets>`
166 * :ref:`Appliance <chap_vm>`
171 * :ref:`Mailing lists <chap_mailinglists>`
172 * `OpenHatch <https://openhatch.org/+projects/NeuroDebian>`_
173 * `Identi.ca <http://identi.ca/neurodebian>`_
174 * `Twitter <http://twitter.com/NeuroDebian>`_
175 * `Google+ <https://plus.google.com/104292290917252528951>`_
176 * `YouTube <http://www.youtube.com/neurodebian>`_
177 * `GitHub <https://github.com/neurodebian>`_
182 * `Debian <http://www.debian.org>`_
183 * `Debian Med <http://www.debian.org/devel/debian-med>`_
184 * `NITRC <http://www.nitrc.org/projects/neurodebian>`_
188 </div><div class="clearer"></div>
207 .. probably should be purged altogether
220 .. include:: link_names.txt
221 .. include:: substitutions.txt
225 <script type="text/javascript">
226 $(document).ready(function($) {
227 //setInterval(function(){
228 $.get('testimonials.html', function(data) {
229 var quotes = $("blockquote", data);
230 var idx = Math.floor(quotes.length * Math.random());
231 $('#randomquote').html(quotes[idx]);
232 }); // update callback
233 //}, 60000); // set interval
235 //$("h1").html("NeuroDebian <span style=\"font-size:14px\">— the ultimate neuroscience software platform</span>")
237 function foldbuttontoggle(foldname) {
238 var foldid = '#' + foldname;
239 var buttonid = foldid + 'button';
240 $(buttonid).on('click', function() {
241 $('#' + foldname).slideToggle();
242 if ($(buttonid).html() == "↓↓↓") {
243 $(buttonid).html("↑↑↑");
246 $(buttonid).html("↓↓↓");
250 $(buttonid).html("↓↓↓");
253 function createvmdownload(rel, mir) {
254 var img_version = '6.0.5';
259 if (rel == 'win32') {
262 img_suffix = 'amd64';
265 base_url = mirrors[mir] + '/vm/';
266 img_url = base_url + 'NeuroDebian_' + img_version + '_' + img_suffix + '.ova';
267 md5sum_url = base_url + 'MD5SUMS';
269 return 'Internal error';
271 return '<blockquote><a href="' + img_url
272 + '">Virtual applicance image</a> [<a title="Verify image integrity by dowloading this file and running `md5sum -c MD5SUMS`" href="'
274 + '">MD5SUM</a>, <a title="Verify authenticity of the MD5SUM file by downloading this file and running `gpg –verify MD5SUMS.gpg`" href="'
275 + md5sum_url + '.gpg">MD5SUM.gpg</a>]</blockquote>' ;
279 function createrepourl(rel, mir) {
280 if(rel in rel2name && mir in mirrors) {
282 var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel2name[rel] + "."
283 + mir + " | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n"
284 + "sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9\n";
289 function updateout(rel, mir) {
290 if (rel != '' && mir != '') {
291 if (rel in {'win32':'', 'win64':'', 'mac':''}) {
292 $('#vmimagedownload').html(createvmdownload(rel, mir));
293 $('#vmsetup').slideDown();
294 $('#reposetup').slideUp();
296 $('#code').text(createrepourl(rel, mir));
297 $('#reposetup').slideDown();
298 $('#vmsetup').slideUp();
303 $('#reposetup').slideUp();
304 $('#vmsetup').slideUp();
307 $('#release').change(function() {
308 var singleValues = $("#release").val();
309 var mirrorVal = $("#mirror").val();
310 updateout(singleValues, mirrorVal);
312 $('#mirror').change(function() {
313 var singleValues = $("#release").val();
314 var mirrorVal = $("#mirror").val();
315 updateout(singleValues, mirrorVal);
318 $(document).ready(function($) {
319 updateout($("#release").val(), $("#mirror").val());
322 foldbuttontoggle('morepublications');