-***********************************************
- Welcome to the Debian Neuroscience Repository
-***********************************************
+.. _WELCOme:
-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 to the Ultimate Platform for Neuroscience
+***************************************************
-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!
+.. quotes::
+ :random: 1
-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>`.
+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. 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.
+
+
+.. 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="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
==========================
-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
+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::
- Thanks to the Department of Experimental Psychology at the University of
- Mageburg, 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`.
+ 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.
-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
+Popularity Contest
+------------------
-Now, you can proceed to install packages, e.g.::
+We would strongly 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 aptitude install lipsia
+ sudo dpkg-reconfigure popularity-contest
.. 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.
+ 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
+========
+
+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>`_
+* `Yaroslav Halchenko <http://www.onerussian.com>`_
+
+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:
+
+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
+
+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]*
+
+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. (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.
-Package authentication
-----------------------
+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>`_]
-When you start using this repository, you probably get warning messages
-like this::
+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.
- The following signatures couldn't be verified because
- the public key is not available.`
+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.
-Or you will be asked questions like this over and over::
+.. _DebConf10: http://debconf10.debconf.org/
+.. _Dartmouth College: http://www.dartmouth.edu/
- 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:
+.. toctree::
+ :hidden:
-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).
+ blog/index
+ faq
+ pkgs
+ spread
+ vm
+ coffeeart
+ photoalbum
+ projects
+ testimonials
-2. Now feed the key into APT by invoking::
+.. probably should be purged altogether
+.. toctree::
+ :hidden:
- apt-key add #file#
+ booth_sfn2010
+ datasets
+ livecd
+ quotes-nihr01
+ quotes-nitrc
+ sources_lists
+ vm_welcome
- 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).
+.. include:: link_names.txt
+.. include:: substitutions.txt
projects / neurodebian.git / blobdiff