X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sphinx%2Findex.rst;h=48e428ae4d0d9ba3adfafaefa8828c3a2636f0a7;hb=65d6e2790e9ddb1e11394b6859b1dc14df440e43;hp=7e21af17c3278f6981d6cfd253953489a467a5ae;hpb=076612138797e09c439796f457b0e8c8f6e8b3fc;p=neurodebian.git diff --git a/sphinx/index.rst b/sphinx/index.rst index 7e21af1..48e428a 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -1,87 +1,258 @@ +.. _WELCOme: + *********************************************** Welcome to the Debian Neuroscience Repository *********************************************** +.. 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 backported or simply rebuilt packages also available +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. +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|. + +.. 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. + + +.. raw:: html -This service is provided "as is". There is no guarantee that a package -works as expected, so use them at your own risk. They might kill your -system (although that is rather unlikely). You've been warned! +

+ + + + + + +

-The repository contains both neuroscience-related packages, as well as general -purpose software which is necessary to resolve dependencies, or such that is -simply useful in the neuroscience context. All featured neuroscience software -packages are available from the :ref:`full package list `. +.. _Ubuntu: http://www.ubuntu.com +.. _news: + +News +==== + +.. 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. + +.. _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: +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:: - If your are interested in mirroring the repository, please see the :ref:`faq`. - -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 +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 proceed to install packages, e.g.:: - - sudo aptitude install lipsia + 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. -Package authentication ----------------------- +.. _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). `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 to be 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 `_] -When you start using this repository, you probably get warning messages -like this:: +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. - The following signatures couldn't be verified because - the public key is not available.` +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. -Or you will be asked questions like this over and over:: +.. _DebConf10: http://debconf10.debconf.org/ +.. _Dartmouth College: http://www.dartmouth.edu/ - WARNING: The following packages cannot be authenticated! - ... - Install these packages without verification [y/N]? -This is because your APT installation initially does not know the GPG -key that is used to sign the release files of this repository. Making -APT happy again is easy: +.. toctree:: + :hidden: -1. Get the key. Either download the `repository key from here - <_static/neuro.debian.net.asc>`_ - or fetch it from http://wwwkeys.pgp.net (2649A5A9). + faq + pkgs + spread + vm + coffeeart + photoalbum + projects + testimonials -2. Now feed the key into APT by invoking:: +.. probably should be purged altogether +.. toctree:: + :hidden: - apt-key add #file# + booth_sfn2010 + datasets + livecd + quotes-nihr01 + quotes-nitrc + sources_lists + vm_welcome - Where `#file#` has to be replaced with the location of the key file you just - downloaded. You need to have superuser-privileges to do this (either do it - as root or use sudo). +.. include:: link_names.txt +.. include:: substitutions.txt