Welcome to the Debian Neuroscience Repository
***********************************************
+.. 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.
+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::
-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 <#contact>`_ them.
+ 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 |spread|, if you like it.
.. raw:: html
<p>
- <a href="pkgs.html"><img border="0" src="_static/package.png" title="List of available packages" /></a>
+ <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>
.. _Ubuntu: http://www.ubuntu.com
+.. _news:
+
News
====
.. raw:: html
- <script src="http://widgets.twimg.com/j/2/widget.js"></script>
- <script>
- new TWTR.Widget({
- version: 2,
- type: 'profile',
- rpp: 10,
- 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 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>
-Follow us on twitter_ to subscribe to the NeuroDebian news.
+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
.. _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:
+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.
.. include:: sources_lists
-.. note::
- Thanks to the `Department of Psychological and Brain Sciences at
- Dartmouth College`_ `[us-nh]` (primary mirror), the `Department of
- Experimental Psychology at the University of Magdeburg`_ `[de]`, and
- the `Medical-image Analysis and Statistical Interpretation lab at
- Vanderbilt`_ `[us-tn]` 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
-.. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
-
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::
+package manager, e.g. synaptic, adept. In the terminal you can use
+:command:`apt-get` to achieve this::
- sudo aptitude update
+ sudo apt-get update
-Now, you can proceed to install packages, e.g.::
+Now, you can install packages, e.g.::
- sudo aptitude install lipsia
+ 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.
-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]?
-
-This is because your APT installation initially does not know the GPG
-key that is used to sign the release files of this repository. It is easy to
-make APT happy again:
-
-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#
-
- 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).
-
-
.. _chap_installation:
-Installation
-============
+Ways to use NeuroDebian
+=======================
-Virtual Machine
+Virtual machine
---------------
If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
computer lab.
-Debian
-------
+Debian installation
+-------------------
Having been exposed to the wonders of NeuroDebian_ you are no longer
satisfied with your previous choice of operating system? We would
.. _chap_team:
-The Team
+The team
========
Our main goal is to provide neuroscience FOSS_ for Debian_. Thus the
express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
for all their work.
-.. _FOSS: http://en.wikipedia.org/wiki/Free_and_open_source_software
+.. _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 the neuroscience software. We will 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
+
+
+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]*
+* `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`.
+
+.. _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
+
+
+Publications
+============
+
+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 to be 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.
-Contact
-=======
+.. _DebConf10: http://debconf10.debconf.org/
+.. _Dartmouth College: http://www.dartmouth.edu/
-`Email us <team@neuro.debian.net>`_ if you have any suggestions or want to
-report a problem.
.. toctree::
:hidden:
pkgs
spread
vm
+ coffeeart
+ photoalbum
+ projects
+ testimonials
.. probably should be purged altogether
.. toctree::
:hidden:
+ booth_sfn2010
+ datasets
livecd
- gpg
- setup
- links_names
- substitutions
+ quotes-nihr01
+ quotes-nitrc
+ sources_lists
+ vm_welcome
-.. include:: links_names.rst
-.. include:: substitutions.rst
+.. include:: link_names.txt
+.. include:: substitutions.txt
projects / neurodebian.git / blobdiff