Merge remote branch 'vm/master'

[neurodebian.git] / sphinx / index.rst

diff --git a/sphinx/index.rst b/sphinx/index.rst
index e802ba6b8da29ab3a1e76d83a0f28abc3b1c59bc..cd9ef575fc5ce2232091dba580b285cf32bed622 100644 (file)
--- a/sphinx/index.rst
+++ b/sphinx/index.rst
@@ -1,33 +1,39 @@
-.. _welcome:
+.. _WELCOme:

 
 ***********************************************
  Welcome to the Debian Neuroscience Repository
 ***********************************************
 
 
 ***********************************************
  Welcome to the Debian Neuroscience Repository
 ***********************************************
 

+.. quotes::
+   :random: 1
+

 This repository provides mostly neuroscience-related packages to be used on
 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
+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
 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>`.
+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. They might kill your
-system (although that is rather unlikely). You've been warned!
+  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.

 
 

-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>`.

 
 .. 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="datasets.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>
  </p>
 
  <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>
  </p>
 

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

 
 News
 ====
 
 News
 ====


@@ -39,7 +45,7 @@ News
  new TWTR.Widget({
    version: 2,
    type: 'profile',
  new TWTR.Widget({
    version: 2,
    type: 'profile',

-   rpp: 10,
+   rpp: 15,

    interval: 6000,
    width: 'auto',
    height: 150,
    interval: 6000,
    width: 'auto',
    height: 150,


@@ -66,8 +72,14 @@ News
  }).render().setUser('NeuroDebian').start();
  </script>
 
  }).render().setUser('NeuroDebian').start();
  </script>
 

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

 .. _repository_howto:
 
 .. _repository_howto:
 

+
+

 How to use this repository
 ==========================
 
 How to use this repository
 ==========================
 


@@ -84,14 +96,24 @@ releases and repository mirrors:
 .. include:: sources_lists
 
 .. note::
 .. 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.
+  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`.
 
 
   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
 .. _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

 
 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
 
 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


@@ -108,56 +130,35 @@ Now, you can proceed to install packages, e.g.::
   about which package version is available for which release and architecture,
   please have a look at the corresponding package pages.
 
   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. Making
-APT happy again is easy:
-
-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).
+After this initial setup you probably also want to configure your package
+manager to recognize the NeuroDebian archive key. With this key the package
+manager can verify that packages haven't been modified and are identical with
+the ones in the main NeuroDebian archive, regardless of which mirror you
+downloaded them from. The NeuroDebian key id is **2649A5A9**. If you need further
+help setting up package authentication, please take a look at
+:ref:`corresponding FAQ <sec_pkg_authentication>`.

 
 
 .. _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


@@ -170,13 +171,13 @@ 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


@@ -184,17 +185,77 @@ 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.
+
+.. _FOSS: http://en.wikipedia.org/wiki/Free_and_open_source_software

 
 

+.. _support:

 
 Contacts
 ========
 
 
 Contacts
 ========
 

-`Email us <team@neuro.debian.net>`_ if you have any suggestions or
-simply |spread| if you liked it.
+`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
+
+.. _neurodebian-users: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users
+.. _neurodebian-devel: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel
+.. _neurodebian-upstream: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-upstream
+
+
+Acknowledgements
+================
+
+We are grateful to Jim Haxby for his continued support and :ref:`endless supply of
+Italian espresso <coffeeart>`.
+
+
+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.
+
+.. _DebConf10: http://debconf10.debconf.org/
+.. _Dartmouth College: http://www.dartmouth.edu/
+

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


@@ -203,16 +264,20 @@ simply |spread| if you liked it.
    pkgs
    spread
    vm
    pkgs
    spread
    vm

-   links_names
-   substitutions
+   coffeeart
+   photoalbum
+   testimonials

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

+   datasets

    livecd
    livecd

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

 
 

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