X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sphinx%2Findex.rst;h=783020fd6157f77325f9164e5880bba9c1ac512c;hb=HEAD;hp=c0c5cf794fbefce245be17cad3d8d11faf3e1131;hpb=b612bc991164a727821d52a9fc129658f1e66f21;p=neurodebian.git diff --git a/sphinx/index.rst b/sphinx/index.rst index c0c5cf7..783020f 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -1,28 +1,19 @@ .. _WELCOme: -*************************************************** - Welcome to the Ultimate Platform for Neuroscience -*************************************************** +********************************************* + 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 :ref:`AFNI `, +:ref:`FSL `, :ref:`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 :ref:`send us an email `. -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 ` 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 -` projects. 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. 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|: +Learn more about NeuroDebian, the goals of this project, and 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 @@ -31,301 +22,107 @@ Please help us |spread|: .. raw:: html -

- - - - - - - -

- -.. _Ubuntu: http://www.ubuntu.com - -.. _news: +
more publications
+
+ +
+
-News -==== +.. quotes:: + :random: 1 .. raw:: html - -
- +
+
more testimonials
-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. - -.. _identi.ca: http://identi.ca/neurodebian -.. _twitter: http://twitter.com/NeuroDebian +.. _Ubuntu: http://www.ubuntu.com .. _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. - -.. raw:: html - -

- -Popularity Contest ------------------- - -We encourage you to participate in the `popularity -contest `_ (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 -`__ or `Ubuntu -`__) you can see/get statistics for -submissions to `NeuroDebian `__ 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. +Get NeuroDebian +=============== +.. include:: reposetup.rst -Debian installation -------------------- +.. _news: -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|. +News +==== +.. raw:: html -.. _chap_team: + + +
+ The news widget requires javascript +
-The team -======== +.. _identi.ca: http://identi.ca/neurodebian +.. _twitter: http://twitter.com/NeuroDebian -`Michael Hanke `_ and `Yaroslav Halchenko -`_ originally started NeuroDebian (formerly the -`Experimental Psychology Debian packaging project -`_) 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. -.. _maintainers: pkgs.html#by-maintainer +.. raw:: html +
+
+ + + + + + +   + +* **About** +* :ref:`The Team ` +* :ref:`FAQ ` +* :ref:`Blog ` +* :ref:`chap_popularity` +* :ref:`chap_publications` +* :ref:`chap_acknowledgements` +* :ref:`testimonials` +* :ref:`coffeeart` + +.. start a new list + +* **Services** +* :ref:`Software ` +* :ref:`Data ` +* :ref:`Appliance ` +* :ref:`Mirrors ` + +.. start a new list + +* **Community** +* :ref:`Contacts ` +* :ref:`Mailing lists ` +* `OpenHatch `_ +* `Identi.ca `_ +* `Twitter `_ +* `Google+ `_ +* `YouTube `_ +* `GitHub `_ + +.. start a new list + +* **Related** +* `Debian `_ +* `Debian Med `_ +* `INCF `_ +* `NITRC `_ -.. _support: - -Contacts -======== +.. raw:: html -`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 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 -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-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) - `_ *[au]* -* Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]* -* Iaroslav Iurchenko *[ua]* -* `Nikolaus Valentin Haenel`_ *[de-v]* - -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 -============ - -Hanke, M. (2012). `Share your tools! But fear the wombat! Seriously. -`_. Talk -given at `Brainhack -`_ 2012 at the -Max-Planck-Institute for Human Cognitive and Brain Sciences*, Leipzig, Germany. -[`video `_] - -Hanke, M. (2012). `Computational and cognitive neuroscience boosted by Debian -OR Just using Debian is not enough -`_. -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 -`_. *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 `_, -Paris, France. - -Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux -`_. -*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 -`_, -Madison, Wisconsin, USA. - -Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at -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. - -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 `_] - -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. - -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. - -.. _DebConf10: http://debconf10.debconf.org/ -.. _Dartmouth College: http://www.dartmouth.edu/ +
+
.. toctree:: @@ -333,26 +130,74 @@ efficient, more open, and more fun blog/index faq + thanks + popularity + about 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 .. include:: link_names.txt .. include:: substitutions.txt + +.. raw:: html + +