X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sphinx%2Findex.rst;h=e6a7bc989ad037e2dcb0bab7f8cac260828ebd4e;hb=b55324a6ebb68967ec6c884b93df01143c91f2b8;hp=6ed382dde8ad1bbfaccb24cf5ef581acb35aa984;hpb=7e146bfb074a1111ea94e752464027e8dcdeb1d6;p=neurodebian.git diff --git a/sphinx/index.rst b/sphinx/index.rst index 6ed382d..e6a7bc9 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -1,72 +1,70 @@ .. _WELCOme: -*********************************************** - Welcome to the Debian Neuroscience Repository -*********************************************** - -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. - -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 |spread|, if you like it. +*************************************************** + Welcome to the Ultimate Platform for Neuroscience +*************************************************** + +.. quotes:: + :random: 1 + +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|: + + 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

- + + + +

.. _Ubuntu: http://www.ubuntu.com +.. _news: + News ==== .. raw:: html - - +
+ -Follow us on twitter_ to subscribe to the NeuroDebian news. +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: @@ -76,92 +74,66 @@ Follow us on twitter_ to subscribe to the NeuroDebian news. 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:: - 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 +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. +.. raw:: html -Package authentication ----------------------- - -When you start using this repository, you probably get warning messages -like this:: - - The following signatures couldn't be verified because - the public key is not available. - -Or you will be asked questions like this over and over:: +

- WARNING: The following packages cannot be authenticated! - ... - Install these packages without verification [y/N]? +Popularity Contest +------------------ -This is because your APT installation initially does not know the GPG -key that is used to sign the release files of this repository. It is easy to -make APT happy again: +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:: -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). + sudo dpkg-reconfigure popularity-contest -2. Now feed the key into APT by invoking:: +.. note:: - apt-key add #file# + 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:: - 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). + 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: -Installation -============ +Ways to use NeuroDebian +======================= -Virtual Machine +Virtual machine --------------- If you are not running Debian_ on a particular machine a :ref:`chap_vm` is @@ -174,8 +146,8 @@ purpose of teaching a neuroimaging data analysis course in a multipurpose computer lab. -Debian ------- +Debian installation +------------------- Having been exposed to the wonders of NeuroDebian_ you are no longer satisfied with your previous choice of operating system? We would @@ -188,27 +160,26 @@ hardware architecture and then simply add |repos|. .. _chap_team: -The 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 `_ 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. -* `Michael Hanke `_ -* `Yaroslav Halchenko `_ +.. _maintainers: pkgs.html#by-maintainer -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 ======== @@ -221,43 +192,167 @@ 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 + 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 -.. _neurodebian-users: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users -.. _neurodebian-devel: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel -.. _neurodebian-upstream: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-upstream - +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 +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]* +* `INCF G-Node at Ludwig-Maximilians-Universität München `_ *[de-m]* + +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:: :hidden: + blog/index faq pkgs spread vm coffeeart + photoalbum + projects + testimonials + testimonials-topics .. probably should be purged altogether .. toctree:: :hidden: + booth_sfn2010 + datasets livecd - gpg - setup - links_names - substitutions + quotes-nihr01 + quotes-nitrc + sources_lists + vm_welcome -.. include:: links_names.rst -.. include:: substitutions.rst +.. include:: link_names.txt +.. include:: substitutions.txt