X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sphinx%2Findex.rst;h=55494d264a6cfbf0458c238ede447ef9497454af;hb=e0e41bbc705dd781a563fa53210b3d36924d9143;hp=b701e712a1a98c86ecdfbc3eb391889febbe3ef9;hpb=41e5654e8bf407844d61747961d8e68633d876ee;p=neurodebian.git diff --git a/sphinx/index.rst b/sphinx/index.rst index b701e71..55494d2 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -1,287 +1,231 @@ .. _WELCOme: -*************************************************** - Welcome to the Ultimate Platform for Neuroscience -*************************************************** +********************************************* + The Ultimate Neuroscience Software Platform +********************************************* -.. quotes:: - :random: 1 - -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 `. 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|. +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>`_. -.. 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. +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 + `_. + *Frontiers in Neuroinformatics*, 6:22. .. raw:: html -

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more publications
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-.. _Ubuntu: http://www.ubuntu.com - -.. _news: - -News -==== +.. quotes:: + :random: 1 .. raw:: html - -
- - -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. +
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more testimonials
-.. _identi.ca: http://identi.ca/neurodebian -.. _twitter: http://twitter.com/NeuroDebian +.. _Ubuntu: http://www.ubuntu.com .. _repository_howto: +.. _chap_installation: +Get NeuroDebian +=============== +First select what kind of operating system you are using, and then choose a +download server close to you: -How to use this repository -========================== +.. include:: sources_lists -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. +.. raw:: html -.. include:: sources_lists +
+ This form requires javascript. If disabled, incomplete instructions are + displayed below
+
+
+ Instructions for Debian-derived systems +
+

Select desired components:
+ + + + + +
only software with guaranteed freedoms
+ all packages are + DSFG-compliant, + with permission to use, modify, re-distribute under any condition
all software
+ + individual packages may have restrictive licenses and you are required to + check license-compliance manually +
+

+ +You can enable NeuroDebian on your system by simply copying and pasting the +following two commands into a terminal window. This will add the NeuroDebian +repository to your native package management system, and you will be able to +install neuroscience software the same way as any other package. + +.. raw:: html + + 
+  After selecting a release the setup code will be shown here.
+
-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`:: +Now you can update the package index and you are ready to install packages. +Of course you can use your favorite package manager (e.g. synaptic, adept) +for this. In the terminal you can use :command:`apt-get`:: sudo apt-get update sudo apt-get install mricron +You are ready to go -- enjoy NeuroDebian! + .. 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 would strongly 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. - - -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|. +
+
+ Instructions for non-Debian systems +
+For all non-Debian operating systems we recommend to deploy NeuroDebian as a +`virtual appliance`_ (virtual machine) -- this will only take a few minutes. +On all modern hardware (built within +the last 3-4 years) a virtual appliance is a convenient solution to run +NeuroDebian simultaneously with the primary operating system -- without +noticeable performance loss. To start using NeuroDebian: -.. _chap_team: +1. Download this image file: +.. raw:: html -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 +2. Import this image into VirtualBox_. If you do not have VirtualBox_ + installed yet, visit the `VirtualBox download page + `_ and get an installer for your + system (installers for Windows, Linux, Mac and Solaris are available). -* `Michael Hanke `_ -* `Yaroslav Halchenko `_ +3. Finish the configuration by following :ref:`the instructions on setting up + the virtual appliance `. `[Virtual machine + setup video tutorial] `_ -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 +You are ready to go -- enjoy NeuroDebian! -* neurodebian-users_: Discussions and support of NeuroDebian users +.. note:: -* 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 + If you still running an older VirtualBox 3.x, download one of the image files + listed below. These older releases are distributed as a `zip` file. Please + extract all files from the `.zip` file, using appropriate software + for your operating system. -* neurodebian-devel_: Technical mailing list for discussions on - NeuroDebian development + * `NeuroDebian 6.0.2 image (32bit) + `_ [~545MB] -You are welcome also to join #neurodebian IRC room on OFTC network if -you have quick questions or want to join a live discussion. + * `NeuroDebian 6.0.2 image (64bit) + `_ [~560MB] -Acknowledgements -================ +.. raw:: html -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 +.. _virtual appliance: http://en.wikipedia.org/wiki/Virtual_appliance +.. _VirtualBox: http://www.virtualbox.org -Thanks to the following institutions and individuals for hosting a mirror: +.. _news: -* `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]* +News +==== -If your are interested in mirroring the repository, please see the :ref:`faq`. +.. raw:: html -.. _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 + +
+ +
+ The news widget requires javascript +
+.. _identi.ca: http://identi.ca/neurodebian +.. _twitter: http://twitter.com/NeuroDebian -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/ +
+
.. toctree:: @@ -292,22 +236,142 @@ 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 + +