3 *********************************************
4 The Ultimate Neuroscience Software Platform
5 *********************************************
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 First select what kind of operating system you are using, and then choose a
47 download server close to you:
49 .. include:: sources_lists
53 <div class="nojavascriptinstructions">
54 This form requires javascript. If disabled, incomplete instructions are
57 <div class="nojavascriptinstructions">
58 Instructions for Debian-derived systems
61 You can enable NeuroDebian on your system by simply copying and pasting the
62 following two commands into a terminal window. This will add the NeuroDebian
63 repository to your native package management system, and you will be able to
64 install neuroscience software the same way as any other package.
69 After selecting a release the setup code will be shown here.
72 Now you can update the package index and you are ready to install packages.
73 Of course you can use your favorite package manager (e.g. synaptic, adept)
74 for this. In the terminal you can use :command:`apt-get`::
77 sudo apt-get install mricron
79 You are ready to go -- enjoy NeuroDebian!
83 Not every package is available for all distributions/releases. For information
84 about which package version is available for which release and architecture,
85 please have a look at the corresponding package pages.
89 </div> <!-- end reposetup -->
92 <div class="nojavascriptinstructions">
93 Instructions for non-Debian systems
96 For all non-Debian operating systems we recommend to deploy NeuroDebian as a
97 `virtual appliance`_ (virtual machine) -- this will only take a few minutes.
98 On all modern hardware (built within
99 the last 3-4 years) a virtual appliance is a convenient solution to run
100 NeuroDebian simultaneously with the primary operating system -- without
101 noticeable performance loss. To start using NeuroDebian:
103 1. Download this image file:
107 <div id="vmimagedownload">
108 <a href="http://neuro.debian.net/debian/vm/">NeuroDebian images</a>
111 2. Import this image into VirtualBox_. If you do not have VirtualBox_
112 installed yet, visit the `VirtualBox download page
113 <http://www.virtualbox.org/wiki/Downloads>`_ and get an installer for your
114 system (installers for Windows, Linux, Mac and Solaris are available).
116 3. Finish the configuration by following :ref:`the instructions on setting up
117 the virtual appliance <chap_vm>`. `[Virtual machine
118 setup video tutorial] <http://www.youtube.com/watch?v=eqfjKV5XaTE>`_
123 You are ready to go -- enjoy NeuroDebian!
127 If you still running an older VirtualBox 3.x, download one of the image files
128 listed below. These older releases are distributed as a `zip` file. Please
129 extract all files from the `.zip` file, using appropriate software
130 for your operating system.
132 * `NeuroDebian 6.0.2 image (32bit)
133 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
135 * `NeuroDebian 6.0.2 image (64bit)
136 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
140 </div> <!-- end vmsetup -->
142 .. _virtual appliance: http://en.wikipedia.org/wiki/Virtual_appliance
143 .. _VirtualBox: http://www.virtualbox.org
152 <script src="_static/jquery.livetwitter.min.js"></script>
153 <div id="identica_widget"></div>
154 <script type="text/javascript">
155 $("#identica_widget").liveTwitter('neurodebian',
156 {service: 'identi.ca',
157 mode: 'user_timeline',
161 <div class="nojavascriptinstructions">
162 The news widget requires javascript
165 .. _identi.ca: http://identi.ca/neurodebian
166 .. _twitter: http://twitter.com/NeuroDebian
175 * :ref:`Team <chap_team>`
176 * :ref:`chap_popularity`
179 * :ref:`chap_publications`
180 * :ref:`testimonials`
186 * :ref:`Software <pkglists>`
187 * :ref:`Data <pkgs-by_purpose-neuroscience_datasets>`
188 * :ref:`Appliance <chap_vm>`
193 * :ref:`Mailing lists <chap_mailinglists>`
194 * `OpenHatch <https://openhatch.org/+projects/NeuroDebian>`_
195 * `Identi.ca <http://identi.ca/neurodebian>`_
196 * `Twitter <http://twitter.com/NeuroDebian>`_
197 * `Google+ <https://plus.google.com/104292290917252528951>`_
198 * `YouTube <http://www.youtube.com/neurodebian>`_
199 * `GitHub <https://github.com/neurodebian>`_
204 * `Debian <http://www.debian.org>`_
205 * `Debian Med <http://www.debian.org/devel/debian-med>`_
206 * `INCF <http://software.incf.org/software/neurodebian>`_
207 * `NITRC <http://www.nitrc.org/projects/neurodebian>`_
211 </div><div class="clearer"></div>
230 .. probably should be purged altogether
243 .. include:: link_names.txt
244 .. include:: substitutions.txt
248 <script type="text/javascript">
249 $(document).ready(function($) {
250 //setInterval(function(){
251 $.get('testimonials.html', function(data) {
252 var quotes = $("blockquote", data);
253 var idx = Math.floor(quotes.length * Math.random());
254 $('#randomquote').html(quotes[idx]);
255 }); // update callback
256 //}, 60000); // set interval
258 //$("h1").html("NeuroDebian <span style=\"font-size:14px\">— the ultimate neuroscience software platform</span>")
260 function foldbuttontoggle(foldname) {
261 var foldid = '#' + foldname;
262 var buttonid = foldid + 'button';
263 $(buttonid).on('click', function() {
264 $('#' + foldname).slideToggle();
265 if ($(buttonid).html() == "↓↓↓") {
266 $(buttonid).html("↑↑↑");
269 $(buttonid).html("↓↓↓");
273 $(buttonid).html("↓↓↓");
276 function createvmdownload(rel, mir) {
277 var img_version = '6.0.5';
282 if (rel == 'win32') {
285 img_suffix = 'amd64';
288 base_url = mirrors[mir] + '/vm/';
289 img_url = base_url + 'NeuroDebian_' + img_version + '_' + img_suffix + '.ova';
290 md5sum_url = base_url + 'MD5SUMS';
292 return 'Internal error';
294 return '<blockquote><a href="' + img_url
295 + '">Virtual applicance image</a> [<a title="Verify image integrity by dowloading this file and running `md5sum -c MD5SUMS`" href="'
297 + '">MD5SUM</a>, <a title="Verify authenticity of the MD5SUM file by downloading this file and running `gpg –verify MD5SUMS.gpg`" href="'
298 + md5sum_url + '.gpg">MD5SUM.gpg</a>]</blockquote>' ;
302 function createrepourl(rel, mir) {
303 if(rel in rel2name && mir in mirrors) {
305 var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel2name[rel] + "."
306 + mir + " | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n"
307 + "sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9\n";
312 function updateout(rel, mir) {
313 if (rel != '' && mir != '') {
314 if (rel in {'win32':'', 'win64':'', 'mac':''}) {
315 $('#vmimagedownload').html(createvmdownload(rel, mir));
316 $('#vmsetup').slideDown();
317 $('#reposetup').slideUp();
319 $('#code').text(createrepourl(rel, mir));
320 $('#reposetup').slideDown();
321 $('#vmsetup').slideUp();
326 $('#reposetup').slideUp();
327 $('#vmsetup').slideUp();
330 $('#release').change(function() {
331 var singleValues = $("#release").val();
332 var mirrorVal = $("#mirror").val();
333 updateout(singleValues, mirrorVal);
335 $('#mirror').change(function() {
336 var singleValues = $("#release").val();
337 var mirrorVal = $("#mirror").val();
338 updateout(singleValues, mirrorVal);
341 $(document).ready(function($) {
342 updateout($("#release").val(), $("#mirror").val());
345 $('#reposetup').hide()