.. _WELCOme:
-***********************************************
- Welcome to the Debian Neuroscience Repository
-***********************************************
+*********************************************
+ The Ultimate Neuroscience Software Platform
+*********************************************
-.. quotes::
- :random: 1
-
-This repository provides mostly neuroscience-related packages to be used on
-Debian_ systems (or Debian-derivatives like Ubuntu_). It contains both unofficial
-or prospective packages which are not (yet) available from the main Debian_
-archive, as well as backported or simply rebuilt packages also available
-elsewhere. Please see the :ref:`faq` for more information about the goals of
-this project, and :ref:`read what people say about it <testimonials>`.
-Take a look at the :ref:`list of our current and planned projects <projects>` if
-you want to get involved. If you appreciate this service, please |spread|.
-
-.. note::
+NeuroDebian provides a large collection of popular neuroscience research
+software for the Debian_ operating system as well as Ubuntu_ and other
+derivatives. Popular packages include FSL, Freesurfer, AFNI, PyMVPA and
+:ref:`many others <pkglists>`. While we do strive to maintain a high level of
+quality, we make no guarantee that a given package works as expected, so use
+them at your own risk. If you do encounter problems or would just like to thank
+us, simply `send us an email <#contacts>`_.
- This service is provided "as is". There is no guarantee that a package
- works as expected, so use them at your own risk. If you encounter problems,
- please `report <#contacts>`_ them.
+Learn more about NeuroDebian, the goals of this project, and help us |spread|!
+ Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
+ next step: An integrated, community-driven computing platform for neuroscience
+ <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_.
+ *Frontiers in Neuroinformatics*, 6:22.
.. raw:: html
- <p>
- <a href="pkgs.html"><img border="0" src="_static/package.png" title="Software package list" /></a>
- <a href="pkglists/pkgs-by_release-datasets_(data).html"><img border="0" src="_static/datasets.png" title="Dataset package list" /></a>
- <a href="vm.html"><img border="0" src="_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /></a>
- <a href="debian/pool"><img border="0" src="_static/pool.png" title="Go to the package pool (deep and cold, only for experts)" /></a>
- <a href="projects.html"><img border="0" src="_static/workarea.png" title="Current and planned projects: Get involved!" /></a>
- <a href="feeds/blog.xml"><img border="0" src="_static/rssfeeds.png" title="NeuroDebian Insider feed" /></a>
- </p>
+ <div class="linkmore"><a href="/publications.html">more publications</a></div>
+ <div class="clearer"></div>
+ <!-- for dynamic quote update via javascript -->
+ <hr />
+ <div id="randomquote" title="Feedback from the community">
-.. _Ubuntu: http://www.ubuntu.com
+.. quotes::
+ :random: 1
-.. _news:
+.. raw:: html
-News
-====
+ </div><!-- randomquote -->
+ <div class="linkmore"><a href="/testimonials.html">more testimonials</a></div>
-.. raw:: html
+.. _Ubuntu: http://www.ubuntu.com
- <script src="_static/jquery.livetwitter.min.js"></script>
- <div id="identica_widget"></div>
- <script type="text/javascript">
- $("#identica_widget").liveTwitter('neurodebian',
- {service: 'identi.ca',
- mode: 'user_timeline',
- limit: 10,
- rate: 300000});
- </script>
+.. _repository_howto:
+.. _chap_installation:
-Older news items are available on identi.ca_. Follow us on identi.ca_
-(preferred) or twitter_ to subscribe to the NeuroDebian news.
+Get NeuroDebian
+===============
-.. _identi.ca: http://identi.ca/neurodebian
-.. _twitter: http://twitter.com/NeuroDebian
+Choose on which operating system you want to run NeuroDebian, and select a
+download server close to you:
-.. _repository_howto:
+.. include:: sources_lists
+.. raw:: html
+ <div id="reposetup" style="display:none">
-How to use this repository
-==========================
+To enable NeuroDebian on your system, simply copy and paste the following
+commands into a terminal window:
-To enable the NeuroDebian repository on your system, select your Debian or
-Ubuntu release and a repository mirror from the lists below. Upon selection
-a short command snippet will be displayed that can be copied and pasted into
-a terminal session. These commands will configure the system package manager
-with the NeuroDebian repository key and package source information.
+.. raw:: html
-.. include:: sources_lists
+ <pre id="code">
+ After selecting a release the setup code will be shown here.
+ </pre>
Once this is done, you have to update the package index and you are ready to
install packages. Use your favorite package manager, e.g. synaptic, adept. In
about which package version is available for which release and architecture,
please have a look at the corresponding package pages.
+.. raw:: html
-.. _chap_installation:
-
-Ways to use NeuroDebian
-=======================
-
-Virtual machine
----------------
-
-If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
-provided as a convenient testing and evaluation environment. After a few
-simple steps to setup the virtual machine, you will be able to use NeuroDebian_
-as an integral part of your existing working environment without any sacrifice.
-The virtual machine is also a suitable environment to temporarily deploy
-neuroscience software on machines running other operating systems, e.g. for the
-purpose of teaching a neuroimaging data analysis course in a multipurpose
-computer lab.
-
-
-Debian installation
--------------------
+ </div> <!-- end reposetup -->
-Having been exposed to the wonders of NeuroDebian_ you are no longer
-satisfied with your previous choice of operating system? We would
-recommend installing Debian_ to replace or complement (dual-boot) your
-existing OS. Please visit `"Getting Debian"
-<http://www.debian.org/distrib/>`_ to obtain the images for your
-hardware architecture and then simply add |repos|.
+ <div id="vmsetup" style="display:none">
+For all non-Debian operating systems the recommended way to deploy NeuroDebian
+is a `virtual appliance`_. On all modern hardware (built within the last 3-4
+years) a virtual appliance is a convenient solution to run NeuroDebian
+simultaneously with the primary operating system -- without noticable
+performance loss.
-.. _chap_team:
+1. Install NeuroDebian by first downloading this image file:
+.. raw:: html
-The team
-========
+ <div id="vmimagedownload">
+ <a href="http://neuro.debian.net/debian/vm/">NeuroDebian images</a>
+ </div>
-Our main goal is to provide neuroscience FOSS_ for Debian_. Thus the
-whole project would not be possible without the work of over 3,000
-Debian_ developers and contributors who are as enthusiastically pursuing
-a similar goal. To add our share -- Debian_ packages of FOSS_ for
-neuroscience research -- the `Experimental Psychology Debian packaging
-project <http://alioth.debian.org/projects/pkg-exppsy>`_ was created
-to formally join the forces of
+2. Once downloaded, import this image into your VirtualBox_ installation. If you
+ do not have VirtualBox_ installed yet, visit the `VirtualBox download page
+ <http://www.virtualbox.org/wiki/Downloads>`_ that provides installers for
+ Windows, Linux, Mac and Solaris.
-* `Michael Hanke <http://mih.voxindeserto.de>`_
-* `Yaroslav Halchenko <http://www.onerussian.com>`_
+3. Please read :ref:`the detailed instructions on setting up the virtual
+ appliance <chap_vm>` to complete the configuration of your NeuroDebian
+ environment.
-A number of packages that are now available from the NeuroDebian repository
-were not packaged by our team, but similar Debian teams. Therefore we want to
-express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
-for all their work.
+.. note::
-.. _support:
+ If you still running an older VirtualBox 3.x, download one of the image files
+ listed below. These older releases are distributed as a `zip` file. Please
+ extract all files from the `.zip` file, using appropriate software
+ for your operating system.
-Contacts
-========
+ * `NeuroDebian 6.0.2 image (32bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
-`Email us directly <team@neuro.debian.net>`_ with any "private"
-communication. Otherwise please use our public mailing lists, which
-exist not only to provide user-support but also to establish
-communication channels within the NeuroDebian community
+ * `NeuroDebian 6.0.2 image (64bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
-* neurodebian-users_: Discussions and support of NeuroDebian users
+.. raw:: html
-* neurodebian-upstream_: General discussions and knowledge sharing
- among developers of the neuroscience software. We will also use it
- to update you with summaries of recent relevant developments in
- Debian project
+ </div> <!-- end vmsetup -->
-* neurodebian-devel_: Technical mailing list for discussions on
- NeuroDebian development
+.. _virtual appliance: http://en.wikipedia.org/wiki/Virtual_appliance
+.. _VirtualBox: http://www.virtualbox.org
+.. _news:
-Acknowledgements
-================
+News
+====
-We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
-Italian espresso <coffeeart>`.
+.. raw:: html
-.. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
+ <script src="_static/jquery.livetwitter.min.js"></script>
+ <div id="identica_widget">[News widget has not been loaded yet]</div>
+ <script type="text/javascript">
+ $("#identica_widget").liveTwitter('neurodebian',
+ {service: 'identi.ca',
+ mode: 'user_timeline',
+ limit: 10,
+ rate: 300000});
+ </script>
-Thanks to the following institutions and individuals for hosting a mirror:
+.. _identi.ca: http://identi.ca/neurodebian
+.. _twitter: http://twitter.com/NeuroDebian
-* `Department of Psychological and Brain Sciences at Dartmouth College`_
- *[us-nh]* (primary mirror)
-* `Department of Experimental Psychology at the University of Magdeburg`_
- *[de]*
-* `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
-* `Paul Ivanov`_ *[us-ca]*
-* `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
- *[us-tn]*
-If your are interested in mirroring the repository, please see the :ref:`faq`.
+.. raw:: html
-.. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
-.. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
-.. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
-.. _Paul Ivanov: http://www.pirsquared.org
-.. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
+ <hr />
+ <div id="sitemap">
+* **About**
+* :ref:`Team <chap_team>`
+* :ref:`chap_popularity`
+* :ref:`FAQ <faq>`
+* :ref:`Blog <blog>`
+* :ref:`chap_publications`
+* :ref:`testimonials`
+* :ref:`coffeeart`
-Publications
-============
+.. start a new list
-Hanke, M. (2011). `Integrating Condor into the Debian operating system
-<_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
-*Talk given at* `CondorWeek 2011
-<http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
-Madison, Wisconsin, USA.
+* **Services**
+* :ref:`Software <pkglists>`
+* :ref:`Data <pkgs-by_purpose-neuroscience_datasets>`
+* :ref:`Appliance <chap_vm>`
-Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
-SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
-Neuroscience*, San Diego, USA.
+.. start a new list
-Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
-(2010). `Having trouble getting your Nature paper? Maybe you are not using the
-right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster to be presented at the
-annual meeting of the Society for Neuroscience*, San Diego, USA.
+* **Community**
+* :ref:`Mailing lists <chap_mailinglists>`
+* `OpenHatch <https://openhatch.org/+projects/NeuroDebian>`_
+* `Identi.ca <http://identi.ca/neurodebian>`_
+* `Twitter <http://twitter.com/NeuroDebian>`_
+* `Google+ <https://plus.google.com/104292290917252528951>`_
+* `YouTube <http://www.youtube.com/neurodebian>`_
+* `GitHub <https://github.com/neurodebian>`_
-Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
-neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
-*Talk given at* DebConf10_, New York City, USA. [video:
-`low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
-`high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
+.. start a new list
-Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
-efficiency in cognitive neuroscience research with NeuroDebian
-<_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
-meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
+* **Related**
+* `Debian <http://www.debian.org>`_
+* `Debian Med <http://www.debian.org/devel/debian-med>`_
+* `INCF <http://software.incf.org/software/neurodebian>`_
+* `NITRC <http://www.nitrc.org/projects/neurodebian>`_
-Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
-statistical learning, and open-source software to make research more
-efficient, more open, and more fun
-<_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
-`Dartmouth College`_, New Hampshire, USA.
+.. raw:: html
-.. _DebConf10: http://debconf10.debconf.org/
-.. _Dartmouth College: http://www.dartmouth.edu/
+ </div><div class="clearer"></div>
+ <hr />
.. toctree::
:hidden:
+ blog/index
faq
pkgs
spread
vm
+ publications
coffeeart
photoalbum
projects
testimonials
+ testimonials-topics
.. probably should be purged altogether
.. toctree::
quotes-nitrc
sources_lists
vm_welcome
+ dump
.. include:: link_names.txt
.. include:: substitutions.txt
+
+.. raw:: html
+
+ <script type="text/javascript">
+ $(document).ready(function($) {
+ //setInterval(function(){
+ $.get('testimonials.html', function(data) {
+ var quotes = $("blockquote", data);
+ var idx = Math.floor(quotes.length * Math.random());
+ $('#randomquote').html(quotes[idx]);
+ }); // update callback
+ //}, 60000); // set interval
+ }); // doc ready
+ //$("h1").html("NeuroDebian <span style=\"font-size:14px\">— the ultimate neuroscience software platform</span>")
+
+ function foldbuttontoggle(foldname) {
+ var foldid = '#' + foldname;
+ var buttonid = foldid + 'button';
+ $(buttonid).on('click', function() {
+ $('#' + foldname).slideToggle();
+ if ($(buttonid).html() == "↓↓↓") {
+ $(buttonid).html("↑↑↑");
+ }
+ else {
+ $(buttonid).html("↓↓↓");
+ }
+ });
+ $(foldid).slideUp();
+ $(buttonid).html("↓↓↓");
+ };
+
+ function createvmdownload(rel, mir) {
+ var img_version = '6.0.5';
+ var img_suffix;
+ var base_url;
+ var img_url;
+ var md5sum_url;
+ if (rel == 'win32') {
+ img_suffix = 'i386';
+ } else {
+ img_suffix = 'amd64';
+ };
+ if(mir in mirrors) {
+ base_url = mirrors[mir] + '/vm/';
+ img_url = base_url + 'NeuroDebian_' + img_version + '_' + img_suffix + '.ova';
+ md5sum_url = base_url + 'MD5SUMS';
+ } else {
+ return 'Internal error';
+ };
+ return '<blockquote><a href="' + img_url
+ + '">Virtual applicance image</a> [<a title="Verify image integrity by dowloading this file and running `md5sum -c MD5SUMS`" href="'
+ + md5sum_url
+ + '">MD5SUM</a>, <a title="Verify authenticity of the MD5SUM file by downloading this file and running `gpg –verify MD5SUMS.gpg`" href="'
+ + md5sum_url + '.gpg">MD5SUM.gpg</a>]</blockquote>' ;
+
+ };
+
+ function createrepourl(rel, mir) {
+ if(rel in rel2name && mir in mirrors) {
+
+ var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel2name[rel] + "."
+ + mir + " | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n"
+ + "sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9\n";
+ return retrepo;
+ }
+
+ };
+ function updateout(rel, mir) {
+ if (rel != '' && mir != '') {
+ if (rel in {'win32':'', 'win64':'', 'mac':''}) {
+ $('#vmimagedownload').html(createvmdownload(rel, mir));
+ $('#vmsetup').slideDown();
+ $('#reposetup').slideUp();
+ } else {
+ $('#code').text(createrepourl(rel, mir));
+ $('#reposetup').slideDown();
+ $('#vmsetup').slideUp();
+ };
+ }
+ else
+ {
+ $('#reposetup').slideUp();
+ $('#vmsetup').slideUp();
+ };
+ };
+ $('#release').change(function() {
+ var singleValues = $("#release").val();
+ var mirrorVal = $("#mirror").val();
+ updateout(singleValues, mirrorVal);
+ });
+ $('#mirror').change(function() {
+ var singleValues = $("#release").val();
+ var mirrorVal = $("#mirror").val();
+ updateout(singleValues, mirrorVal);
+ });
+
+ $(document).ready(function($) {
+ updateout($("#release").val(), $("#mirror").val());
+ });
+
+ foldbuttontoggle('morepublications');
+
+
+ </script>
+
+