.. _WELCOme:
-*************
- NeuroDebian
-*************
+*********************************************
+ The Ultimate Neuroscience Software Platform
+*********************************************
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
+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 would just like to thank
-us, simply `send us an email <#contacts>`_.
+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>`.
Learn more about NeuroDebian, the goals of this project, and help us |spread|!
.. raw:: html
+ <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">
.. raw:: html
</div><!-- randomquote -->
+ <div class="linkmore"><a href="testimonials.html">more testimonials</a></div>
.. _Ubuntu: http://www.ubuntu.com
Get NeuroDebian
===============
-Make your selection to enable NeuroDebian on your computer:
-
-.. include:: sources_lists
-
-.. raw:: html
-
- <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
-the terminal you can use :command:`apt-get`::
-
- sudo apt-get update
- sudo apt-get install mricron
-
-.. 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.
-
-.. raw:: html
-
- </div> <!-- end reposetup -->
-
- <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
-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
--------------------
-
-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|.
-
-.. raw:: html
-
- </div> <!-- end vmsetup -->
+.. include:: reposetup.rst
.. _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>
+ <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>
-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.
+ <div class="nojavascriptinstructions">
+ The news widget requires javascript
+ </div>
.. _identi.ca: http://identi.ca/neurodebian
.. _twitter: http://twitter.com/NeuroDebian
-
-
-.. _support:
-
-Contacts
-========
-
-`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-users_: Discussions and support of NeuroDebian users
-
-* neurodebian-upstream_: General discussions and knowledge sharing
- among developers of neuroscience software. We also use it
- to update you with summaries of recent relevant developments in
- Debian project
-
-* neurodebian-devel_: Technical mailing list for discussions on
- NeuroDebian development
-
-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
-================
-
-We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
-Italian espresso <coffeeart>`.
-
-.. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
-
-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-md]*
-* `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
-* `Paul Ivanov`_ *[us-ca]*
-* `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
- *[us-tn]*
-* `Australia's research and education network (AARNET)
- <http://www.aarnet.edu.au>`_ *[au]*
-* Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
-* Iaroslav Iurchenko *[ua]*
-* `Nikolaus Valentin Haenel`_ *[de-v]*
-
-If your are interested in mirroring the repository, please see the :ref:`faq`.
-
-.. _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
-.. _Nikolaus Valentin Haenel: http://haenel.co
-
-
-Publications
-============
-
-Hanke, M. (2012). `Share your tools! But fear the wombat! Seriously.
-<http://neuro.debian.net/_files/Hanke_FearTheWombat_Brainhack2012.pdf>`_ *Talk
-given at* `Brainhack <http://brainhack.org/2012/04/06/brainhack-2012-unconference>`_ 2012 at the
-Max-Planck-Institute for Human Cognitive and Brain Sciences*, Leipzig, Germany.
-[`video <http://youtu.be/8t6znEOEDVo>`_]
-
-Hanke, M. (2012). `Computational and cognitive neuroscience boosted by Debian
-OR Just using Debian is not enough
-<http://neuro.debian.net/_files/Hanke_UsingDebianIsNotEnough_ESRF2012.pdf>`_.
-Talk given at the workshop "Debian for Scientific Facilities Days" at the
-European Synchrotron Radiation Facility (ESRF), Grenoble, France.
-
-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
- <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*,
-University of Edinburgh, Edinburgh, UK.
-
-Halchenko, Y. O. & Hanke, M. (2012). `Environments for efficient
-contemporary research in neuroimaging: PyMVPA and NeuroDebian
-<_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
-*Talk given at the University of Pennsylvania School of Medicine*,
-Philadelphia, PA, USA.
-
-Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
-NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
-*Talk given at the Max-Planck-Institute for Human Cognitive and Brain
-Sciences*, Leipzig, Germany.
-
-Hanke, M. (2011). `More than batteries included: NeuroDebian
-<_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
-*Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,
-Paris, France.
-
-Halchenko, Y. O. (2011). `π's in Debian or Scientific Debian: NumPy, SciPy and beyond
-<_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
-*Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
-Paris, France.
-
-Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
-<http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
-*Frontiers in Neuroinformatics, 5:8*.
-
-Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
-platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
-*Poster presented at the annual meeting of the Organisation for Human Brain
-Mapping*, Quebec City, Canada.
-
-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.
-
-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.
-
-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 presented at the
-annual meeting of the Society for Neuroscience*, San Diego, USA.
-
-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>`_]
-
-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.
-
-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
-
- </div>
-
-.. _DebConf10: http://debconf10.debconf.org/
-.. _Dartmouth College: http://www.dartmouth.edu/
-
-Popularity
-==========
+ <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
- <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.
+ </div><div class="clearer"></div>
+ <hr />
.. toctree::
blog/index
faq
+ thanks
+ popularity
+ about
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:
- booth_sfn2010
- datasets
livecd
quotes-nihr01
quotes-nitrc
- sources_lists
- vm_welcome
.. include:: link_names.txt
.. include:: substitutions.txt
<script type="text/javascript">
$(document).ready(function($) {
- setInterval(function(){
+ //setInterval(function(){
$.get('testimonials.html', function(data) {
var quotes = $("blockquote", data);
var idx = Math.floor(quotes.length * Math.random());
$('#randomquote').html(quotes[idx]);
}); // update callback
- }, 60000); // set interval
+ //}, 60000); // set interval
}); // doc ready
//$("h1").html("NeuroDebian <span style=\"font-size:14px\">— the ultimate neuroscience software platform</span>")
$(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