X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sphinx%2Findex.rst;h=9417d3748f10d45c233a5678eef1967e4aada4fd;hb=7ed7de6426ba7bb92e5ee76ec372d6a8a7c6dcfe;hp=24c3bbd9d9cd5404f222b6acae04b95d43a428e8;hpb=cb0012051cf9f794b6b1649479c72bed89f3fafb;p=neurodebian.git diff --git a/sphinx/index.rst b/sphinx/index.rst index 24c3bbd..9417d37 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -1,27 +1,33 @@ .. _WELCOme: -*********************************************** - Welcome to the Debian Neuroscience Repository -*********************************************** +*************************************************** + Welcome to the Ultimate Platform for Neuroscience +*************************************************** .. 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 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|. - -.. 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. - +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 @@ -31,7 +37,8 @@ you want to get involved. If you appreciate this service, please |spread|. - + +

.. _Ubuntu: http://www.ubuntu.com @@ -53,8 +60,9 @@ News rate: 300000}); -Older news items are available on identi.ca_. Follow us on identi.ca_ -(preferred) or 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 @@ -67,7 +75,7 @@ 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 +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. @@ -87,6 +95,38 @@ the terminal you can use :command:`apt-get`:: 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: @@ -123,21 +163,21 @@ hardware architecture and then simply add |repos|. 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. .. _support: @@ -152,13 +192,15 @@ 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 +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 ================ @@ -173,11 +215,17 @@ 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]* + *[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`. @@ -186,18 +234,82 @@ If your are interested in mirroring the repository, please see the :ref:`faq`. .. _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 ============ +Halchenko, Y.O. and Hanke, M. (2013). `Open is not enough: benefits from Debian as an integrated, community-driven computing platform. +`_ *Talk +given at* `SEA-2013 `_ +conference, University Corporation for Atmospheric Research (UCAR), Boulder CO, USA. + +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 to be presented at 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 @@ -224,6 +336,7 @@ efficient, more open, and more fun .. toctree:: :hidden: + blog/index faq pkgs spread @@ -232,6 +345,7 @@ efficient, more open, and more fun photoalbum projects testimonials + testimonials-topics .. probably should be purged altogether .. toctree::