.. _WELCOme:
-***********************************************
- Welcome to the Debian Neuroscience Repository
-***********************************************
+***************************************************
+ Welcome to the Ultimate Platform for Neuroscience
+***************************************************
.. 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, 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 <#contacts>`_ them.
-
+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
<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>
==========================
To enable the NeuroDebian repository on your system, select your Debian or
-Ubuntu release and a repository mirror from the lists below. Upon selection
+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.
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:
The team
========
-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
-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
+`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.
-* `Michael Hanke <http://mih.voxindeserto.de>`_
-* `Yaroslav Halchenko <http://www.onerussian.com>`_
+.. _maintainers: pkgs.html#by-maintainer
-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
-express particular gratitude to the `Debian Med`_ and `Debian Science`_ teams
-for all their work.
.. _support:
* 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
+ among developers of neuroscience software. We also use it
to update you with summaries of recent relevant developments in
Debian project
* `Department of Psychological and Brain Sciences at Dartmouth College`_
*[us-nh]* (primary mirror)
* `Department of Experimental Psychology at the University of Magdeburg`_
- *[de]*
+ *[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`.
.. _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
============
+Halchenko, Y.O. and Hanke, M. (2013). `Open is not enough: benefits from Debian as an integrated, community-driven computing platform.
+<http://neuro.debian.net/_files/Halchenko_OpenIsNotEnough_UCAR2013.pdf>`_ *Talk
+given at* `SEA-2013 <http://sea.ucar.edu/event/open-not-enough-benefits-debian-integrated-community-driven-computing-platform>`_
+conference*, University Corporation for Atmospheric Research (UCAR), Boulder CO, USA.
+
+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>`_,
photoalbum
projects
testimonials
+ testimonials-topics
.. probably should be purged altogether
.. toctree::
projects / neurodebian.git / blobdiff