.. _WELCOme:
-***********************************************
- Welcome to the Debian Neuroscience Repository
-***********************************************
+*********************************************
+ The Ultimate Neuroscience Software Platform
+*********************************************
-.. quotes::
- :random: 1
+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 <pkg_tocs>`. 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 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>`.
-If you appreciate this service, please |spread|.
-
-.. note::
-
- 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="datasets.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>
- </p>
-
-.. _Ubuntu: http://www.ubuntu.com
+ <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">
-News
-====
+.. quotes::
+ :random: 1
.. raw:: html
- <script src="http://widgets.twimg.com/j/2/widget.js"></script>
- <script>
- new TWTR.Widget({
- version: 2,
- type: 'profile',
- rpp: 15,
- interval: 6000,
- width: 'auto',
- height: 150,
- theme: {
- shell: {
- background: '#898989',
- color: '#ffffff'
- },
- tweets: {
- background: '#ffffff',
- color: '#000000',
- links: '#82032f'
- }
- },
- features: {
- scrollbar: true,
- loop: false,
- live: false,
- hashtags: true,
- timestamp: true,
- avatars: false,
- behavior: 'all'
- }
- }).render().setUser('NeuroDebian').start();
- </script>
-
-Follow us on twitter_ to subscribe to the NeuroDebian news.
+ </div><!-- randomquote -->
+ <div class="linkmore"><a href="/testimonials.html">more testimonials</a></div>
-.. _twitter: http://twitter.com/NeuroDebian
+.. _Ubuntu: http://www.ubuntu.com
.. _repository_howto:
+.. _chap_installation:
+Get NeuroDebian
+===============
-
-How to use this repository
-==========================
-
-The easiest way to use this repository is to download an APT-configuration file
-(`sources.list`). Simply choose your target distribution/release and download
-the configuration for a mirror close to you (depending on your browser, you
-might have to right-click and choose 'save as'). Once downloaded, put the file
-in the `/etc/apt/sources.list.d/` directory on your system. Moving files in
-this directory will require superuser privileges, therefore you should probably
-download the file into a temporary directory and subsequently move it into
-`/etc/apt/sources.list.d/`. APT-configurations are available for the following
-releases and repository mirrors:
+First select what kind of operating system you are using, and then choose a
+download server close to you:
.. include:: sources_lists
-.. note::
- Thanks to the following institutions and individuals for hosting a mirror:
-
- * `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]*
+.. raw:: html
- If your are interested in mirroring the repository, please see the :ref:`faq`.
+ <div class="nojavascriptinstructions">
+ This form requires javascript. If disabled, incomplete instructions are
+ displayed below</div>
+ <div id="repoconfig">
+ <div class="nojavascriptinstructions">
+ Instructions for Debian-derived systems
+ </div>
+ <p>Select desired components:<br />
+ <table><tr>
+ <td><input type="radio" name="components" value="libre"></td>
+ <td><strong>only</strong> software with guaranteed freedoms<br />
+ <span style=font-size:75%>all packages are
+ <a href="http://www.debian.org/social_contract#guidelines">DSFG</a>-compliant,
+ with permission to use, modify, re-distribute under any condition</span></td></tr>
+ <tr><td><input type="radio" name="components" value="full"></td>
+ <td>all software<br />
+ <span style=font-size:75%>
+ individual packages may have restrictive licenses and you are required to
+ check license-compliance manually
+ </span></td></tr>
+ </table>
+ <div id="reposetup">
+
+You can enable NeuroDebian on your system by simply copying and pasting the
+following two commands into a terminal window. This will add the NeuroDebian
+repository to your native package management system, and you will be able to
+install neuroscience software the same way as any other package.
-.. _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
+.. raw:: html
-Once this is done, you have to update the package index. Use your favorite
-package manager, e.g. synaptic, adept, or whatever you like. In the terminal
-you can use :command:`aptitude` to achieve the same::
+ <pre id="code">
+ After selecting a release the setup code will be shown here.
+ </pre>
- sudo aptitude update
+Now you can update the package index and you are ready to install packages.
+Of course you can use your favorite package manager (e.g. synaptic, adept)
+for this. In the terminal you can use :command:`apt-get`::
-Now, you can proceed to install packages, e.g.::
+ sudo apt-get update
+ sudo apt-get install mricron
- sudo aptitude install lipsia
+You are ready to go -- enjoy NeuroDebian!
.. note::
+
Not every package is available for all distributions/releases. For information
about which package version is available for which release and architecture,
please have a look at the corresponding package pages.
-After this initial setup you probably also want to configure your package
-manager to recognize the NeuroDebian archive key. With this key the package
-manager can verify that packages haven't been modified and are identical with
-the ones in the main NeuroDebian archive, regardless of which mirror you
-downloaded them from. The NeuroDebian key id is **2649A5A9**. If you need further
-help setting up package authentication, please take a look at
-:ref:`corresponding FAQ <sec_pkg_authentication>`.
+.. raw:: html
+ </div> <!-- end reposetup -->
+ </div> <!-- end repoconfig -->
-.. _chap_installation:
+ <div id="vmsetup">
+ <div class="nojavascriptinstructions">
+ Instructions for non-Debian systems
+ </div>
-Ways to use NeuroDebian
-=======================
+For all non-Debian operating systems we recommend to deploy NeuroDebian as a
+`virtual appliance`_ (virtual machine) -- this will only take a few minutes.
+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
+noticeable performance loss. To start using NeuroDebian:
-Virtual machine
----------------
+1. Download this image file:
-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.
+.. raw:: html
+ <div id="vmimagedownload">
+ <a href="http://neuro.debian.net/debian/vm/">NeuroDebian images</a>
+ </div>
-Debian installation
--------------------
+2. Import this image into VirtualBox_. If you do not have VirtualBox_
+ installed yet, visit the `VirtualBox download page
+ <http://www.virtualbox.org/wiki/Downloads>`_ and get an installer for your
+ system (installers for Windows, Linux, Mac and Solaris are available).
-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|.
+3. Finish the configuration by following :ref:`the instructions on setting up
+ the virtual appliance <chap_vm>`. `[Virtual machine
+ setup video tutorial] <http://www.youtube.com/watch?v=eqfjKV5XaTE>`_
-.. _chap_team:
-The team
-========
+You are ready to go -- enjoy NeuroDebian!
-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
+.. note::
-* `Michael Hanke <http://mih.voxindeserto.de>`_
-* `Yaroslav Halchenko <http://www.onerussian.com>`_
+ 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.
-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.
+ * `NeuroDebian 6.0.2 image (32bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
-.. _FOSS: http://en.wikipedia.org/wiki/Free_and_open_source_software
+ * `NeuroDebian 6.0.2 image (64bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
+.. raw:: html
-Contacts
-========
+ </div> <!-- end vmsetup -->
-`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
+.. _virtual appliance: http://en.wikipedia.org/wiki/Virtual_appliance
+.. _VirtualBox: http://www.virtualbox.org
-* neurodebian-users_: Discussions and support of NeuroDebian users
+.. _news:
-* 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
+News
+====
-* neurodebian-devel_: Technical mailing list for discussions on
- NeuroDebian development
+.. raw:: html
-.. _neurodebian-users: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users
-.. _neurodebian-devel: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel
-.. _neurodebian-upstream: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-upstream
+ <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>
+ <div class="nojavascriptinstructions">
+ The news widget requires javascript
+ </div>
+.. _identi.ca: http://identi.ca/neurodebian
+.. _twitter: http://twitter.com/NeuroDebian
+
+
+.. raw:: html
+
+ <hr />
+ <div id="sitemap">
-Acknowledgements
-================
+* **About**
+* :ref:`Team <chap_team>`
+* :ref:`chap_popularity`
+* :ref:`FAQ <faq>`
+* :ref:`Blog <blog>`
+* :ref:`chap_publications`
+* :ref:`testimonials`
+* :ref:`coffeeart`
-We are grateful to Jim Haxby for his continued support and :ref:`endless supply of
-Italian espresso <coffeeart>`.
+.. start a new list
+* **Services**
+* :ref:`Software <pkg_tocs>`
+* :ref:`Data <toc_pkgs_for_suite_data>`
+* :ref:`Appliance <chap_vm>`
-Publications
-============
+.. 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? *Poster to be presented at the anual 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
+ vm_welcome
+ derivatives
+
+.. are these supposed to be visible?
+.. toctree::
+ :hidden:
+
+ machines
+ todo
+
+.. toctree::
+ :hidden:
+ :glob:
+
+ pkgs/*
+ pkglists/*
.. probably should be purged altogether
.. toctree::
:hidden:
livecd
- gpg
- setup
- links_names
- substitutions
quotes-nihr01
quotes-nitrc
+ dump
+
+.. include:: link_names.txt
+.. include:: substitutions.txt
-.. include:: links_names.rst
-.. include:: substitutions.rst
+.. 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, comp) {
+ if(mir in mirrors) {
+ var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel + "."
+ + mir + "." + comp + " | 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 update_by_form() {
+ var rel = $("#release").val();
+ var mir = $("#mirror").val();
+ var comp = $('input[name="components"]:checked').val();
+ if (rel != '' && mir != '') {
+ if (rel in {'win32':'', 'win64':'', 'mac':''}) {
+ $('#vmimagedownload').html(createvmdownload(rel, mir));
+ $('#vmsetup').slideDown();
+ $('#repoconfig').slideUp();
+ } else {
+ $('#vmsetup').slideUp();
+ $('#repoconfig').slideDown();
+ if (comp == undefined) {
+ $('#reposetup').slideUp();
+ } else {
+ $('#code').text(createrepourl(rel, mir, comp));
+ $('#reposetup').slideDown();
+ }
+ };
+ }
+ else
+ {
+ $('#repoconfig').slideUp();
+ $('#vmsetup').slideUp();
+ };
+ };
+
+ $(document).ready(function($) {
+ update_by_form();
+ $('#repoconfig').hide()
+ $('#reposetup').hide();
+ $('#vmsetup').hide()
+ $('#release').change(update_by_form);
+ $('#mirror').change(update_by_form);
+ $('input[name=components]:radio').change(update_by_form);
+ });
+
+ </script>
projects / neurodebian.git / blobdiff