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 <pkg_tocs>`. 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
60 <p>Select desired components:<br />
62 <td><input type="radio" name="components" value="libre"></td>
63 <td><strong>only</strong> software with guaranteed freedoms<br />
64 <span style=font-size:75%>all packages are
65 <a href="http://www.debian.org/social_contract#guidelines">DSFG</a>-compliant,
66 with permission to use, modify, re-distribute under any condition</span></td></tr>
67 <tr><td><input type="radio" name="components" value="full"></td>
68 <td>all software<br />
69 <span style=font-size:75%>
70 individual packages may have restrictive licenses and you are required to
71 check license-compliance manually
76 You can enable NeuroDebian on your system by simply copying and pasting the
77 following two commands into a terminal window. This will add the NeuroDebian
78 repository to your native package management system, and you will be able to
79 install neuroscience software the same way as any other package.
84 After selecting a release the setup code will be shown here.
87 Now you can update the package index and you are ready to install packages.
88 Of course you can use your favorite package manager (e.g. synaptic, adept)
89 for this. In the terminal you can use :command:`apt-get`::
92 sudo apt-get install mricron
94 You are ready to go -- enjoy NeuroDebian!
98 Not every package is available for all distributions/releases. For information
99 about which package version is available for which release and architecture,
100 please have a look at the corresponding package pages.
104 </div> <!-- end reposetup -->
105 </div> <!-- end repoconfig -->
108 <div class="nojavascriptinstructions">
109 Instructions for non-Debian systems
112 For all non-Debian operating systems we recommend to deploy NeuroDebian as a
113 `virtual appliance`_ (virtual machine) -- this will only take a few minutes.
114 On all modern hardware (built within
115 the last 3-4 years) a virtual appliance is a convenient solution to run
116 NeuroDebian simultaneously with the primary operating system -- without
117 noticeable performance loss. To start using NeuroDebian:
119 1. Download this image file:
123 <div id="vmimagedownload">
124 <a href="http://neuro.debian.net/debian/vm/">NeuroDebian images</a>
127 2. Import this image into VirtualBox_. If you do not have VirtualBox_
128 installed yet, visit the `VirtualBox download page
129 <http://www.virtualbox.org/wiki/Downloads>`_ and get an installer for your
130 system (installers for Windows, Linux, Mac and Solaris are available).
132 3. Finish the configuration by following :ref:`the instructions on setting up
133 the virtual appliance <chap_vm>`. `[Virtual machine
134 setup video tutorial] <http://www.youtube.com/watch?v=eqfjKV5XaTE>`_
139 You are ready to go -- enjoy NeuroDebian!
143 If you still running an older VirtualBox 3.x, download one of the image files
144 listed below. These older releases are distributed as a `zip` file. Please
145 extract all files from the `.zip` file, using appropriate software
146 for your operating system.
148 * `NeuroDebian 6.0.2 image (32bit)
149 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
151 * `NeuroDebian 6.0.2 image (64bit)
152 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
156 </div> <!-- end vmsetup -->
158 .. _virtual appliance: http://en.wikipedia.org/wiki/Virtual_appliance
159 .. _VirtualBox: http://www.virtualbox.org
168 <script src="_static/jquery.livetwitter.min.js"></script>
169 <div id="identica_widget"></div>
170 <script type="text/javascript">
171 $("#identica_widget").liveTwitter('neurodebian',
172 {service: 'identi.ca',
173 mode: 'user_timeline',
177 <div class="nojavascriptinstructions">
178 The news widget requires javascript
181 .. _identi.ca: http://identi.ca/neurodebian
182 .. _twitter: http://twitter.com/NeuroDebian
191 * :ref:`Team <chap_team>`
192 * :ref:`chap_popularity`
195 * :ref:`chap_publications`
196 * :ref:`testimonials`
202 * :ref:`Software <pkg_tocs>`
203 * :ref:`Data <toc_pkgs_for_suite_data>`
204 * :ref:`Appliance <chap_vm>`
209 * :ref:`Mailing lists <chap_mailinglists>`
210 * `OpenHatch <https://openhatch.org/+projects/NeuroDebian>`_
211 * `Identi.ca <http://identi.ca/neurodebian>`_
212 * `Twitter <http://twitter.com/NeuroDebian>`_
213 * `Google+ <https://plus.google.com/104292290917252528951>`_
214 * `YouTube <http://www.youtube.com/neurodebian>`_
215 * `GitHub <https://github.com/neurodebian>`_
220 * `Debian <http://www.debian.org>`_
221 * `Debian Med <http://www.debian.org/devel/debian-med>`_
222 * `INCF <http://software.incf.org/software/neurodebian>`_
223 * `NITRC <http://www.nitrc.org/projects/neurodebian>`_
227 </div><div class="clearer"></div>
248 .. are these supposed to be visible?
262 .. probably should be purged altogether
271 .. include:: link_names.txt
272 .. include:: substitutions.txt
276 <script type="text/javascript">
277 $(document).ready(function($) {
278 //setInterval(function(){
279 $.get('testimonials.html', function(data) {
280 var quotes = $("blockquote", data);
281 var idx = Math.floor(quotes.length * Math.random());
282 $('#randomquote').html(quotes[idx]);
283 }); // update callback
284 //}, 60000); // set interval
286 //$("h1").html("NeuroDebian <span style=\"font-size:14px\">— the ultimate neuroscience software platform</span>")
288 function foldbuttontoggle(foldname) {
289 var foldid = '#' + foldname;
290 var buttonid = foldid + 'button';
291 $(buttonid).on('click', function() {
292 $('#' + foldname).slideToggle();
293 if ($(buttonid).html() == "↓↓↓") {
294 $(buttonid).html("↑↑↑");
297 $(buttonid).html("↓↓↓");
301 $(buttonid).html("↓↓↓");
304 function createvmdownload(rel, mir) {
305 var img_version = '6.0.5';
310 if (rel == 'win32') {
313 img_suffix = 'amd64';
316 base_url = mirrors[mir] + '/vm/';
317 img_url = base_url + 'NeuroDebian_' + img_version + '_' + img_suffix + '.ova';
318 md5sum_url = base_url + 'MD5SUMS';
320 return 'Internal error';
322 return '<blockquote><a href="' + img_url
323 + '">Virtual applicance image</a> [<a title="Verify image integrity by dowloading this file and running `md5sum -c MD5SUMS`" href="'
325 + '">MD5SUM</a>, <a title="Verify authenticity of the MD5SUM file by downloading this file and running `gpg –verify MD5SUMS.gpg`" href="'
326 + md5sum_url + '.gpg">MD5SUM.gpg</a>]</blockquote>' ;
330 function createrepourl(rel, mir, comp) {
332 var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel + "."
333 + mir + "." + comp + " | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n"
334 + "sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9\n";
340 function update_by_form() {
341 var rel = $("#release").val();
342 var mir = $("#mirror").val();
343 var comp = $('input[name="components"]:checked').val();
344 if (rel != '' && mir != '') {
345 if (rel in {'win32':'', 'win64':'', 'mac':''}) {
346 $('#vmimagedownload').html(createvmdownload(rel, mir));
347 $('#vmsetup').slideDown();
348 $('#repoconfig').slideUp();
350 $('#vmsetup').slideUp();
351 $('#repoconfig').slideDown();
352 if (comp == undefined) {
353 $('#reposetup').slideUp();
355 $('#code').text(createrepourl(rel, mir, comp));
356 $('#reposetup').slideDown();
362 $('#repoconfig').slideUp();
363 $('#vmsetup').slideUp();
367 $(document).ready(function($) {
369 $('#repoconfig').hide()
370 $('#reposetup').hide();
372 $('#release').change(update_by_form);
373 $('#mirror').change(update_by_form);
374 $('input[name=components]:radio').change(update_by_form);