.. _WELCOme:
-***************************************************
- Welcome to the Ultimate Platform for Neuroscience
-***************************************************
+*************
+ NeuroDebian
+*************
-.. 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 <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>`_.
-NeuroDebian provides a turnkey software platform for neuroscience
-that is created by integrating research tools with the Debian_ operating
-system. If you are using such software on Debian_ or its derivatives,
-such as Ubuntu_, chances are that you are already using NeuroDebian.
-
-This website provides a :ref:`supplementary repository <repository_howto>` with
-both unofficial or prospective packages which are not (yet) available from the
-main Debian_ archive, as well as backported or simply rebuilt latest versions
-of software. NeuroDebian serves as an "upstream" to some :ref:`derivative
-<chap_derivatives>` projects. 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. 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.
-Please help us |spread|:
+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
.. 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="derivatives.html"><img border="0" src="_static/derivatives.png" title="NeuroDebian Derivatives" /></a>
- <a href="blog/index.html"><img border="0" src="_static/rssfeeds.png" title="NeuroDebian Insider Blog" /></a>
- </p>
-
-.. _Ubuntu: http://www.ubuntu.com
-
-.. _news:
+ <!-- for dynamic quote update via javascript -->
+ <hr />
+ <div id="randomquote" title="Feedback from the community">
-News
-====
+.. quotes::
+ :random: 1
.. raw:: html
- <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><!-- randomquote -->
-For more news and information see our :ref:`blog <blog>`. Older news items are
-available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to
-subscribe to the NeuroDebian news.
-
-.. _identi.ca: http://identi.ca/neurodebian
-.. _twitter: http://twitter.com/NeuroDebian
+.. _Ubuntu: http://www.ubuntu.com
.. _repository_howto:
+.. _chap_installation:
+Get NeuroDebian
+===============
+Make your selection to enable NeuroDebian on your computer:
-How to use this repository
-==========================
+.. include:: sources_lists
-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
+ <div id="reposetup" style="display:none">
+
+ <p>Copy and paste the following command into a terminal window:</p>
+ <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
.. raw:: html
- <p><img border="0" src="_files/nd_subscriptionstats.png" title="Statistics of new repository subscriptions for all supported releases. Note: subscription is only done once per machine." /></p>
+ </div> <!-- end reposetup -->
-Popularity Contest
-------------------
-
-We encourage you to participate in the `popularity
-contest <http://popcon.debian.org>`_ (popcon), which anonymously
-collects the list of packages you installed/use on your system.
-Collecting such statistics is of particular importance for research
-software projects as a prove of an existing user-base. If upon
-installation of the system you rejected the invitation to participate
-you can always change your decision by running::
-
- sudo dpkg-reconfigure popularity-contest
-
-.. note::
-
- If you are deploying multiple systems through cloning, to not have
- all systems considered as one, it would be necessary to re-generate
- the random MY_HOSTID. Following commands ran as root should do it
- (as root) without any interactive dialog::
-
- sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
- DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
-
-In addition to popcon pages for your "core" distribution (e.g. `Debian
-<http://popcon.debian.org/>`__ or `Ubuntu
-<http://popcon.ubuntu.com/>`__) you can see/get statistics for
-submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
-know that you are already contributing back to the community.
-
-.. _chap_installation:
-
-Ways to use NeuroDebian
-=======================
-
-Virtual machine
----------------
+ <div id="vmsetup" style="display:none">
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
<http://www.debian.org/distrib/>`_ to obtain the images for your
hardware architecture and then simply add |repos|.
+.. raw:: html
-.. _chap_team:
+ </div> <!-- end vmsetup -->
+.. _news:
-The team
-========
+News
+====
+
+.. raw:: html
+
+ <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>
+
+For more news and information see our :ref:`blog <blog>`. Older news items are
+available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to
+subscribe to the NeuroDebian news.
+
+.. _identi.ca: http://identi.ca/neurodebian
+.. _twitter: http://twitter.com/NeuroDebian
-`Michael Hanke <http://mih.voxindeserto.de>`_ and `Yaroslav Halchenko
-<http://www.onerussian.com>`_ originally started NeuroDebian (formerly the
-`Experimental Psychology Debian packaging project
-<http://alioth.debian.org/projects/pkg-exppsy>`_) and are the current project
-leaders. However, the whole project would not be possible without the work of
-over 3,000 Debian_ developers and contributors who are as enthusiastically
-building the Debian operating system.
-A number of packages that are available from the NeuroDebian repository have
-been contributed by various individuals and other teams in Debian, such as
-`Debian Med`_ and `Debian Science`_. We want to express our gratitude to all
-maintainers_ that help to make Debian_ the ultimate software platform for
-neuroscience.
-.. _maintainers: pkgs.html#by-maintainer
.. _support:
You are welcome also to join #neurodebian IRC room on OFTC network if
you have quick questions or want to join a live discussion.
+.. _chap_team:
+
+The team
+========
+
+`Michael Hanke <http://mih.voxindeserto.de>`_ and `Yaroslav Halchenko
+<http://www.onerussian.com>`_ originally started NeuroDebian (formerly the
+`Experimental Psychology Debian packaging project
+<http://alioth.debian.org/projects/pkg-exppsy>`_) and are the current project
+leaders. However, the whole project would not be possible without the work of
+over 3,000 Debian_ developers and contributors who are as enthusiastically
+building the Debian operating system.
+A number of packages that are available from the NeuroDebian repository have
+been contributed by various individuals and other teams in Debian, such as
+`Debian Med`_ and `Debian Science`_. We want to express our gratitude to all
+maintainers_ that help to make Debian_ the ultimate software platform for
+neuroscience.
+
+.. _maintainers: pkgs.html#by-maintainer
+
+
Acknowledgements
================
<http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_. *Frontiers in Neuroinformatics*,
6:22.
+.. raw:: html
+
+ <span id="morepublicationsbutton" class="button" title="Click to toogle more"></span>
+ <div id="morepublications">
+
Hanke, M. (2012). `The why and how of getting packaged
<_files/Hanke_GetPackaged_CodeJam5_2012.pdf>`_.
*Talk given at BrainScaleS CodeJam 5, Convergence in Computational Neuroscience*,
<_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
`Dartmouth College`_, New Hampshire, USA.
+.. raw:: html
+
+ </div>
+
.. _DebConf10: http://debconf10.debconf.org/
.. _Dartmouth College: http://www.dartmouth.edu/
+Popularity
+==========
+
+.. raw:: html
+
+ <p><img border="0" src="_files/nd_subscriptionstats.png" title="Statistics of new repository subscriptions for all supported releases. Note: subscription is only done once per machine." /></p>
+
+Popularity Contest
+------------------
+
+We encourage you to participate in the `popularity
+contest <http://popcon.debian.org>`_ (popcon), which anonymously
+collects the list of packages you installed/use on your system.
+Collecting such statistics is of particular importance for research
+software projects as a prove of an existing user-base. If upon
+installation of the system you rejected the invitation to participate
+you can always change your decision by running::
+
+ sudo dpkg-reconfigure popularity-contest
+
+.. note::
+
+ If you are deploying multiple systems through cloning, to not have
+ all systems considered as one, it would be necessary to re-generate
+ the random MY_HOSTID. Following commands ran as root should do it
+ (as root) without any interactive dialog::
+
+ sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
+ DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
+
+In addition to popcon pages for your "core" distribution (e.g. `Debian
+<http://popcon.debian.org/>`__ or `Ubuntu
+<http://popcon.ubuntu.com/>`__) you can see/get statistics for
+submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
+know that you are already contributing back to the community.
+
.. toctree::
:hidden:
.. 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 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 != '') {
+ $('#code').text(createrepourl(rel, mir));
+ if (rel in {'win':'', 'rel':''}) {
+ $('#vmsetup').slideDown();
+ $('#reposetup').slideUp();
+ } else {
+ $('#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);
+ });
+
+
+ foldbuttontoggle('morepublications');
+
+
+ </script>
+
+
projects / neurodebian.git / blobdiff