Merge pull request #9 from zyv/master

[neurodebian.git] / sphinx / index.rst

.. _WELCOme:

***************************************************
 Welcome to the Ultimate Platform for Neuroscience
***************************************************

.. quotes::
   :random: 1

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|:

  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

 <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:

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

.. _repository_howto:



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

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

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

 <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.

.. _chap_installation:

Ways to use NeuroDebian
=======================

Virtual machine
---------------

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|.


.. _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


.. _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-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]*
* `INCF G-Node at Ludwig-Maximilians-Universität München <http://www.g-node.org>`_ *[de-m]*

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.

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/


.. toctree::
   :hidden:

   blog/index
   faq
   pkgs
   spread
   vm
   coffeeart
   photoalbum
   projects
   testimonials
   testimonials-topics

.. 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