X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sphinx%2Findex.rst;h=ed4a6c4650eb52192d9c269d49b946534b308650;hb=be409bf8567f0215613d6a25f33c6b7941864bf3;hp=71177d6a3c361e2378769dd037cec3da03d709cd;hpb=5dd559531fc5e1e30ca45b9e16ec399123434b97;p=neurodebian.git diff --git a/sphinx/index.rst b/sphinx/index.rst index 71177d6..ed4a6c4 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -1,41 +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 would just like to thank +us, 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 @@ -52,201 +61,58 @@ News limit: 10, rate: 300000}); - -For more news and information see our :ref:`blog `. Older news items are -available on identi.ca_. Follow us on identi.ca_ (preferred) 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 -========================== - -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. - - -.. _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. - -.. _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 - -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 `. - -.. _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]* - -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. +.. raw:: html -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 `_, -Paris, France. +
+
-Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux -`_. -*Frontiers in Neuroinformatics, 5:8*. +* **About** +* :ref:`Team ` +* :ref:`chap_popularity` +* :ref:`FAQ ` +* :ref:`Blog ` +* :ref:`chap_publications` +* :ref:`testimonials` +* :ref:`coffeeart` -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. +.. start a new list -Hanke, M. (2011). `Integrating Condor into the Debian operating system -<_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_. -*Talk given at* `CondorWeek 2011 -`_, -Madison, Wisconsin, USA. +* **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 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:: @@ -257,22 +123,69 @@ efficient, more open, and more fun 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: - booth_sfn2010 - datasets livecd quotes-nihr01 quotes-nitrc - sources_lists - vm_welcome + dump .. include:: link_names.txt .. include:: substitutions.txt + +.. raw:: html + +