-.. _welcome:
+.. _WELCOme:
-***********************************************
- Welcome to the Debian Neuroscience Repository
-***********************************************
+*********************************************
+ The Ultimate Neuroscience Software Platform
+*********************************************
-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 backported or simply rebuilt packages also available
-elsewhere. Please see the :ref:`faq` for more information about the goals of
-this project.
+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 :ref:`AFNI <binary_pkg_afni>`,
+:ref:`FSL <binary_pkg_fsl-complete>`, :ref:`PyMVPA <binary_pkg_python-mvpa2>` 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 you just like to say
+thanks, simply :ref:`send us an email <chap_contacts>`.
-This service is provided "as is". There is no guarantee that a package
-works as expected, so use them at your own risk. They might kill your
-system (although that is rather unlikely). You've been warned!
+Learn more about NeuroDebian, the goals of this project, and help us |spread|!
-The repository contains both neuroscience-related packages, as well as general
-purpose software which is necessary to resolve dependencies, or such that is
-simply useful in the neuroscience context. All featured neuroscience software
-packages are available from the :ref:`full package list <full_pkg_list>`.
-
-News
-====
+ 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
- <script src="http://widgets.twimg.com/j/2/widget.js"></script>
- <script>
- new TWTR.Widget({
- version: 2,
- type: 'profile',
- rpp: 4,
- 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>
-
-.. _repository_howto:
-
-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:
-
-.. include:: sources_lists
-
-.. note::
- Thanks to the `Department of Experimental Psychology at the University of
- Magdeburg`_, and the `Department of Psychological and Brain Sciences at Dartmouth
- College`_ for hosting a mirror.
-
- If your are interested in mirroring the repository, please see the :ref:`faq`.
-
-.. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
-.. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
-
-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::
-
- sudo aptitude update
-
-Now, you can proceed to install packages, e.g.::
-
- sudo aptitude install lipsia
-
-.. 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.
-
-
-Package authentication
-----------------------
-
-When you start using this repository, you probably get warning messages
-like this::
-
- The following signatures couldn't be verified because
- the public key is not available.`
-
-Or you will be asked questions like this over and over::
-
- WARNING: The following packages cannot be authenticated!
- ...
- Install these packages without verification [y/N]?
+ <div class="linkmore"><a href="publications.html" name="publications">more publications</a></div>
+ <div class="clearer"></div>
+ <!-- for dynamic quote update via javascript -->
+ <hr />
+ <div id="randomquote" title="Feedback from the community">
-This is because your APT installation initially does not know the GPG
-key that is used to sign the release files of this repository. Making
-APT happy again is easy:
+.. quotes::
+ :random: 1
-1. Get the key. Either download the `repository key from here
- <_static/neuro.debian.net.asc>`_
- or fetch it from http://wwwkeys.pgp.net (2649A5A9).
-
-2. Now feed the key into APT by invoking::
-
- apt-key add #file#
+.. raw:: html
- Where `#file#` has to be replaced with the location of the key file you just
- downloaded. You need to have superuser-privileges to do this (either do it
- as root or use sudo).
+ </div><!-- randomquote -->
+ <div class="linkmore"><a href="testimonials.html">more testimonials</a></div>
+.. _Ubuntu: http://www.ubuntu.com
+.. _repository_howto:
.. _chap_installation:
-Installation
-============
-
-Virtual Machine
----------------
-
-If your are not running a 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.
+Get NeuroDebian
+===============
+.. include:: reposetup.rst
-Debian
-------
+.. _news:
-Having being 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|.
+News
+====
+.. raw:: html
-.. _chap_team:
+ <a class="twitter-timeline" href="https://twitter.com/NeuroDebian"
+ data-widget-id="360194288006606848"
+ data-link-color="#820430"
+ height="150px"
+ data-show-replies="false"
+ data-chrome="noheader nofooter transparent">Tweets by @NeuroDebian</a>
+ <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
+ <div class="nojavascriptinstructions">
+ The news widget requires javascript
+ </div>
-The Team
-========
+.. _identi.ca: http://identi.ca/neurodebian
+.. _twitter: http://twitter.com/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 share
-our goal. To provide our share -- Debian_ packages of FOSS for
-neuroscience research -- `Experimental Psychology Debian packaging
-project <http://alioth.debian.org/projects/pkg-exppsy>`_ was created
-to formally join the forces of
-* `Michael Hanke <http://mih.voxindeserto.de>`_
-* `Yaroslav Halchenko <http://www.onerussian.com>`_
+.. raw:: html
-Some packages provided within NeuroDebian repository were not packaged
-by our team, but were provided by similar Debian teams. Therefore we
-want to express particular gratitude to `Debian Med`_ and `Debian
-Science`_ teams for making our job easier.
+ <hr />
+ <div id="sitemap">
+ <!-- Some anchors to orient users of old-website urls -->
+ <a name="acknowledgements"/>
+ <a name="contacts"/>
+ <a name="the-team"/>
+ <a name="debian-installation"/>
+ <a name="virtual-machine"/>
+ <a name="ways-to-use-neurodebian"> </a>
+
+* **About**
+* :ref:`The Team <chap_team>`
+* :ref:`FAQ <faq>`
+* :ref:`Blog <blog>`
+* :ref:`chap_popularity`
+* :ref:`chap_publications`
+* :ref:`chap_acknowledgements`
+* :ref:`testimonials`
+* :ref:`coffeeart`
+
+.. start a new list
+
+* **Services**
+* :ref:`Software <pkg_tocs>`
+* :ref:`Data <toc_pkgs_for_release_data>`
+* :ref:`Appliance <chap_vm>`
+* :ref:`Mirrors <chap_mirrors_stats>`
+
+.. start a new list
+
+* **Community**
+* :ref:`Contacts <chap_contacts>`
+* :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>`_
+
+.. start a new list
+
+* **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>`_
+.. raw:: html
-Contacts
-========
+ </div><div class="clearer"></div>
+ <hr />
-`Email us <team@neuro.debian.net>`_ if you have any suggestions or
-simply |spread| if you liked it.
.. toctree::
:hidden:
+ blog/index
faq
+ thanks
+ popularity
+ about
pkgs
spread
vm
- links_names
- substitutions
+ 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
+ quotes-nihr01
+ quotes-nitrc
+
+.. include:: link_names.txt
+.. include:: substitutions.txt
+
+.. raw:: html
-.. include:: links_names.rst
-.. include:: substitutions.rst
+ <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("↓↓↓");
+ };
+
+ </script>
projects / neurodebian.git / blobdiff