X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sphinx%2Findex.rst;h=30626ea14407d4de6fed790729db50434ef8e2ba;hb=aa26bd2b62184eb7d7356fb86d243c8550e6ff2d;hp=47be6279da7a7fc3e30b0f3300fca7241c6551c6;hpb=56fde2f99569b83e9b21c157793518e6ab6ba10d;p=neurodebian.git diff --git a/sphinx/index.rst b/sphinx/index.rst index 47be627..30626ea 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -1,40 +1,50 @@ .. _WELCOme: -*********************************************** - Welcome to the Debian Neuroscience Repository -*********************************************** +********************************************* + The Ultimate Neuroscience Software Platform +********************************************* -.. quotes:: - :random: 1 +NeuroDebian provides a large collection of popular neuroscience research +software for the Debian_ operating system as well as Ubuntu_ and other +derivatives. Popular packages include FSL, Freesurfer, AFNI, PyMVPA and +:ref:`many others `. While we do strive to maintain a high level of +quality, we make no guarantee that a given package works as expected, so use +them at your own risk. If you do encounter problems or you just like to say +thanks, simply `send us an email <#contacts>`_. -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 `. -Take a look at the :ref:`list of our current and planned projects ` if -you want to get involved. If you appreciate this service, please |spread|. +Learn more about NeuroDebian, the goals of this project, and help us |spread|! -.. note:: + Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the + next step: An integrated, community-driven computing platform for neuroscience + `_. + *Frontiers in Neuroinformatics*, 6:22. - 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 +
more publications
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more testimonials
.. _Ubuntu: http://www.ubuntu.com +.. _repository_howto: +.. _chap_installation: + +Get NeuroDebian +=============== + +.. include:: reposetup.rst + .. _news: News @@ -42,241 +52,140 @@ News .. raw:: html - - +
+ - -Follow us on identi.ca_ or twitter_ to subscribe to the NeuroDebian news. +
+ The news widget requires javascript +
.. _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: - -.. include:: sources_lists - -.. note:: - 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`. - -.. _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 -you can use :command:`aptitude` to achieve the same:: - - sudo aptitude update - -Now, you can proceed to install packages, e.g.:: - - sudo aptitude install lipsia - -.. 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 `. - - -.. _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" -`_ 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 `_ was created -to formally join the forces of - -* `Michael Hanke `_ -* `Yaroslav Halchenko `_ - -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. - -.. _FOSS: http://en.wikipedia.org/wiki/Free_and_open_source_software - -.. _support: - -Contacts -======== - -`Email us directly `_ 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 +.. raw:: html -Acknowledgements -================ +
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-We are grateful to Jim Haxby for his continued support and :ref:`endless supply of -Italian espresso `. +* **About** +* :ref:`Team ` +* :ref:`chap_popularity` +* :ref:`FAQ ` +* :ref:`Blog ` +* :ref:`chap_publications` +* :ref:`testimonials` +* :ref:`coffeeart` +.. start a new list -Publications -============ +* **Services** +* :ref:`Software ` +* :ref:`Data ` +* :ref:`Appliance ` -Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at -SfN2010 `. *Annual meeting of the Society for -Neuroscience*, San Diego, USA. +.. start a new list -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. +* **Community** +* :ref:`Mailing lists ` +* `OpenHatch `_ +* `Identi.ca `_ +* `Twitter `_ +* `Google+ `_ +* `YouTube `_ +* `GitHub `_ -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 `_, -`high resolution `_] +.. start a new list -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. +* **Related** +* `Debian `_ +* `Debian Med `_ +* `INCF `_ +* `NITRC `_ -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. +.. raw:: html -.. _DebConf10: http://debconf10.debconf.org/ -.. _Dartmouth College: http://www.dartmouth.edu/ +
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.. toctree:: :hidden: + blog/index faq pkgs spread vm + publications coffeeart photoalbum + projects testimonials + testimonials-topics + vm_welcome + derivatives + +.. are these supposed to be visible? +.. toctree:: + :hidden: + + machines + todo + +.. toctree:: + :hidden: + :glob: + + pkgs/* + pkglists/* .. probably should be purged altogether .. toctree:: :hidden: - datasets livecd - vm_welcome quotes-nihr01 quotes-nitrc - + dump .. include:: link_names.txt .. include:: substitutions.txt + +.. raw:: html + +