.. _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
<p>
<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="
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
.. raw:: html
- <script src="http://widgets.twimg.com/j/2/widget.js"></script>
- <script>
- new TWTR.Widget({
- version: 2,
- type: 'profile',
- rpp: 15,
- 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>
-Follow us on identi.ca_ or 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
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
-.. note::
- Thanks to the following institutions and individuals for hosting a mirror:
+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`::
- * `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]*
+ sudo apt-get update
+ sudo apt-get install mricron
- If your are interested in mirroring the repository, please see the :ref:`faq`.
+.. note::
-.. _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
+ 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::
+.. 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>
- sudo aptitude update
+Popularity Contest
+------------------
-Now, you can proceed to install packages, e.g.::
+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 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.
-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>`.
+ 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>`_
-* `Yaroslav Halchenko <http://www.onerussian.com>`_
+`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.
-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.
+.. _maintainers: pkgs.html#by-maintainer
-.. _FOSS: http://en.wikipedia.org/wiki/Free_and_open_source_software
.. _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
* 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
+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
============
+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>`_,
+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 to be presented at 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
.. 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
- vm_welcome
quotes-nihr01
quotes-nitrc
-
+ sources_lists
+ vm_welcome
.. include:: link_names.txt
.. include:: substitutions.txt
projects / neurodebian.git / blobdiff