adjustments to quotes-nihr01.rst (before I realized that it was auto-generated :-/)

[neurodebian.git] / sphinx / index.rst

diff --git a/sphinx/index.rst b/sphinx/index.rst
index f61cf245ca21cb10d15d23d6b2cf7b2f9dfe954d..4b616fb78e5c6c0f1c58bc0b1f3c729e96aca10d 100644 (file)
--- a/sphinx/index.rst
+++ b/sphinx/index.rst
@@ -1,73 +1,69 @@
-.. _welcome:
-
-***********************************************
- Welcome to the Debian Neuroscience Repository
-***********************************************
-
-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.
-
+.. _WELCOme:
+
+***************************************************
+ Welcome to the Ultimate Platform for Neuroscience
+***************************************************
+
+.. quotes::
+   :random: 1
+
+The NeuroDebian project provides a turnkey platform for neuroscience
+through integrating of related software within the Debian_ operating
+system.  If you are using neuroscience-related software which
+comes with you installation of Debian_ or its derivative, such as
+Ubuntu_, good chance is that you are already *using NeuroDebian*.
+
+This website provides an additional repository with both unofficial
+or prospective packages which are not (yet) available from the main
+Debian_ archive, as well as backported or simply rebuilt newest
+versions of packages.
+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. If you
+appreciate this service, please |spread|.

 This service is provided "as is". There is no guarantee that a package
 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!
-
-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>`.
+works as expected, so use them at your own risk. If you encounter problems,
+please `report <#contacts>`_ them.

 
 .. raw:: html
 
  <p>
 
 .. 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="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>
 
  </p>
 

+.. _Ubuntu: http://www.ubuntu.com
+
+.. _news:

 
 News
 ====
 
 .. raw:: html
 
 
 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>
 
  </script>
 

-Follow us on twitter_ to subscribe to the NeuroDebian news.
+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
 
 .. _repository_howto:
 .. _twitter: http://twitter.com/NeuroDebian
 
 .. _repository_howto:


@@ -77,93 +73,80 @@ Follow us on twitter_ to subscribe to the NeuroDebian news.
 How to use this repository
 ==========================
 
 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
 
 
 .. 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.::
+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 aptitude install lipsia
+  sudo apt-get update
+  sudo apt-get install mricron

 
 .. note::
 
 .. 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.
 
   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

 
 

-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::
+ <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>

 
 

-  WARNING: The following packages cannot be authenticated!
-  ...
-  Install these packages without verification [y/N]?
+Popularity Contest
+------------------

 
 

-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:
+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::

 
 

-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).
+ sudo dpkg-reconfigure popularity-contest

 
 

-2. Now feed the key into APT by invoking::
+.. note::

 
 

-     apt-key add #file#
+   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::

 
 

-   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).
+    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:
 
 
 .. _chap_installation:
 

-Installation
-============
+Ways to use NeuroDebian
+=======================

 
 

-Virtual Machine
+Virtual machine

 ---------------
 
 ---------------
 

-If your 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.
+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
-------
+Debian installation
+-------------------

 
 Having been exposed to the wonders of NeuroDebian_ you are no longer
 satisfied with your previous choice of operating system?  We would
 
 Having been exposed to the wonders of NeuroDebian_ you are no longer
 satisfied with your previous choice of operating system?  We would


@@ -176,13 +159,13 @@ hardware architecture and then simply add |repos|.
 .. _chap_team:
 
 
 .. _chap_team:
 
 

-The Team
+The team

 ========
 
 ========
 

-Our main goal is to provide neuroscience FOSS for Debian_. Thus the
+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
 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
+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
 neuroscience research -- the `Experimental Psychology Debian packaging
 project <http://alioth.debian.org/projects/pkg-exppsy>`_ was created
 to formally join the forces of


@@ -190,35 +173,164 @@ to formally join the forces of
 * `Michael Hanke <http://mih.voxindeserto.de>`_
 * `Yaroslav Halchenko <http://www.onerussian.com>`_
 
 * `Michael Hanke <http://mih.voxindeserto.de>`_
 * `Yaroslav Halchenko <http://www.onerussian.com>`_
 

-A number of packages that are now provided within the NeuroDebian repository
+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
 were not packaged by our team, but similar Debian teams.  Therefore we want to

-express particular gratitude to `Debian Med`_ and `Debian Science`_ teams for
-all their work.
+express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
+for all their work.

 
 

+.. _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.
+
+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]*
+* `Australia's research and education network (AARNET)
+  <http://www.aarnet.edu.au>`_ *[au]*
+* Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
+* Iaroslav Iurchenko *[ua]*
+
+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
+============

 
 

-Contact
-=======
+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.
+
+.. _DebConf10: http://debconf10.debconf.org/
+.. _Dartmouth College: http://www.dartmouth.edu/

 
 

-`Email us <team@neuro.debian.net>`_ if you have any suggestions or
-simply |spread| if you liked it.

 
 .. toctree::
    :hidden:
 
 
 .. toctree::
    :hidden:
 

+   blog/index

    faq
    pkgs
    spread
    vm
    faq
    pkgs
    spread
    vm

-   links_names
-   substitutions
+   coffeeart
+   photoalbum
+   projects
+   testimonials

 
 .. probably should be purged altogether
 .. toctree::
    :hidden:
 
 
 .. probably should be purged altogether
 .. toctree::
    :hidden:
 

+   booth_sfn2010
+   datasets

    livecd
    livecd

-   gpg
-   setup
+   quotes-nihr01
+   quotes-nitrc
+   sources_lists
+   vm_welcome

 
 

-.. include:: links_names.rst
-.. include:: substitutions.rst
+.. include:: link_names.txt
+.. include:: substitutions.txt