From: Michael Hanke Date: Fri, 7 Dec 2012 08:38:03 +0000 (+0100) Subject: Merge branch 'master' into newdesign X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=1f3e1e3baea966d60a549aaa16e5e03ad890a473;hp=daa9f4b4c6fabcdd1abe8b53d760a7ece4681e01;p=neurodebian.git Merge branch 'master' into newdesign * master: updated VM page for 6.0.6 (with the date when VM was wrapped on 1st of Oct) add remake to give it a page Conflicts: sphinx/vm.rst --- diff --git a/artwork/config.svg b/artwork/config.svg new file mode 100644 index 0000000..b8fe600 --- /dev/null +++ b/artwork/config.svg @@ -0,0 +1,192 @@ + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + diff --git a/artwork/debian.svg b/artwork/debian.svg new file mode 100644 index 0000000..d23a4b5 --- /dev/null +++ b/artwork/debian.svg @@ -0,0 +1,278 @@ + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/artwork/faq.svg b/artwork/faq.svg new file mode 100644 index 0000000..493b775 --- /dev/null +++ b/artwork/faq.svg @@ -0,0 +1,432 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + diff --git a/artwork/feedback.svg b/artwork/feedback.svg new file mode 100644 index 0000000..f7de496 --- /dev/null +++ b/artwork/feedback.svg @@ -0,0 +1,561 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/artwork/neurodebian.svg b/artwork/neurodebian.svg new file mode 100644 index 0000000..f877aae --- /dev/null +++ b/artwork/neurodebian.svg @@ -0,0 +1,335 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + diff --git a/artwork/nitrc.svg b/artwork/nitrc.svg new file mode 100644 index 0000000..7735073 --- /dev/null +++ b/artwork/nitrc.svg @@ -0,0 +1,6345 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/neurodebian/templates/sources_lists.rst b/neurodebian/templates/sources_lists.rst index f56d610..58de169 100644 --- a/neurodebian/templates/sources_lists.rst +++ b/neurodebian/templates/sources_lists.rst @@ -1,26 +1,21 @@ .. raw:: html -
- 
- After selecting a release the setup code will be shown here.
-
-
- diff --git a/sphinx/_static/config.png b/sphinx/_static/config.png new file mode 100644 index 0000000..e60f10c Binary files /dev/null and b/sphinx/_static/config.png differ diff --git a/sphinx/_static/debian.png b/sphinx/_static/debian.png new file mode 100644 index 0000000..0e19be0 Binary files /dev/null and b/sphinx/_static/debian.png differ diff --git a/sphinx/_static/demo_button.png b/sphinx/_static/demo_button.png new file mode 100644 index 0000000..c7cfa11 Binary files /dev/null and b/sphinx/_static/demo_button.png differ diff --git a/sphinx/_static/faq.png b/sphinx/_static/faq.png new file mode 100644 index 0000000..adca7c8 Binary files /dev/null and b/sphinx/_static/faq.png differ diff --git a/sphinx/_static/feedback.png b/sphinx/_static/feedback.png new file mode 100644 index 0000000..0d1d8a5 Binary files /dev/null and b/sphinx/_static/feedback.png differ diff --git a/sphinx/_static/hotbrain_bg.jpg b/sphinx/_static/hotbrain_bg.jpg new file mode 100644 index 0000000..771a5ed Binary files /dev/null and b/sphinx/_static/hotbrain_bg.jpg differ diff --git a/sphinx/_static/neurodebian.css b/sphinx/_static/neurodebian.css index e5e3d06..b0d643b 100644 --- a/sphinx/_static/neurodebian.css +++ b/sphinx/_static/neurodebian.css @@ -5,7 +5,7 @@ body { font-family: sans-serif; font-size: 100%; - background-color: #444; + background-color: #fff; color: #000; margin: 0; padding: 0; @@ -14,7 +14,7 @@ body { /* :::: LAYOUT :::: */ div.document { - background-color: #afafaf; + background-color: #fff; } div.documentwrapper { @@ -28,6 +28,10 @@ div.bodywrapper { div.body { background-color: white; + background-image: url(hotbrain_bg.jpg); + background-repeat:no-repeat; + background-position:100% 100%; + background-attachment:fixed; padding: 0 20px 30px 20px; } @@ -71,24 +75,20 @@ div.clearer { } div.footer { - color: #fff; + color: #000; width: 100%; padding: 9px 0 9px 0; text-align: center; font-size: 75%; } -div.footer a { - color: #fff; - text-decoration: underline; -} - div.related { background-color: #2c3c3d; - color: #fff; + color: #888; width: 100%; line-height: 30px; font-size: 90%; + float: right; } div.related h3 { @@ -111,7 +111,7 @@ div.related li.right { } div.related a { - color: white; + color: #fff; } /* ::: TOC :::: */ @@ -218,6 +218,10 @@ ul.search li div.context { text-align: left; } +ul.simple { + margin-bottom: 1em; +} + ul.keywordmatches li.goodmatch a { font-weight: bold; } @@ -335,7 +339,7 @@ div.body h4, div.body h5, div.body h6 { font-family: 'Trebuchet MS', sans-serif; - background-color: #f2f2f2; + background-color: rgba(242, 242, 242, 0.5); font-weight: normal; color: #20435c; border-bottom: 1px solid #ccc; @@ -343,7 +347,7 @@ div.body h6 { padding: 3px 0 3px 10px; } -div.body h1 { margin-top: 0; font-size: 200%; } +div.body h1 { margin-top: 0em; font-size: 180%; padding-top: 1em;} div.body h2 { font-size: 160%; } div.body h3 { font-size: 140%; } div.body h4 { font-size: 120%; } @@ -477,7 +481,7 @@ div.warning { } div.note { - background-color: #eaf2f9; + background-color: rgba(234, 242, 249, 0.6); border: 1px solid #3d7aa5; border-left: none; border-right: none; @@ -552,6 +556,11 @@ dd { color: #060; } +dt { + font-weight: bold; + margin-top: 1em; +} + dt:target, .highlight { background-color: #fbe54e; @@ -569,7 +578,7 @@ th { pre { padding: 5px; - background-color: #efc; + background-color: rgba(238, 255, 204, 0.6); color: #333; border: 1px solid #ac9; border-left: none; @@ -784,5 +793,112 @@ td.task { text-align: left; } +.button { + background-color: transparent; + font-weight: normal; + color: #20435c; + border: 1px solid #ccc; + padding: 3px; + text-align: center; + cursor: pointer; +} + +div.buttonbar { + background-color: #fff; + font-size: 70%; +} +div.buttonbar a:hover { + text-decoration: none; +} + +div.buttonbar a:hover img { + background-color: #ffc7da; +} + +div.buttonbar ul { + list-style: none; + padding: 0px; +} + +div.buttonbar li { + display: inline; + float: left; + margin: 5px; + text-align: center; +} +div#randomquote { +} + +div#randomquote blockquote.epigraph { + padding: 0 2em 2em 2em; + background-color: transparent; + font-style: italic; + font-size: 80%; + border: 0px +} + +#troubleshooting dt, +div#frequently-asked-questions dt { + font-weight: bold; + margin-top: 1em; + margin-left: 1em; + cursor: pointer; + display: list-item; + list-style-image:url(neurodebian_bullet.png); +} + +div#frequently-asked-questions dt:after { + content: "\203A\203A"; + padding-left: .25em; +} + +div#sitemap ul { + float: left; + list-style: none; +} + +.linkmore { + margin-top: -2em; + float: right; + font-size: 70%; +} + +.nojavascriptinstructions { + font-size: 70%; +} + +.expandinstructions { + font-size: 70%; + display: none; +} + +.linkmore:before, +.nojavascriptinstructions:before, +.expandinstructions:before { + content: "[" +} + +.linkmore:after, +.nojavascriptinstructions:after, +.expandinstructions:after { + content: "]" +} + + +.highlighted { + background-color: yellow; +} + +#searchbox p { + display: inline; +} + +.inlineimage { + vertical-align: baseline; +} + +a img.inlineimage:hover { + background-color: #820430; +} diff --git a/sphinx/_static/neurodebian.png b/sphinx/_static/neurodebian.png new file mode 100644 index 0000000..d88a9e6 Binary files /dev/null and b/sphinx/_static/neurodebian.png differ diff --git a/sphinx/_static/nitrc.png b/sphinx/_static/nitrc.png new file mode 100644 index 0000000..ca4bc05 Binary files /dev/null and b/sphinx/_static/nitrc.png differ diff --git a/sphinx/_static/video_button.png b/sphinx/_static/video_button.png new file mode 100644 index 0000000..dff08a1 Binary files /dev/null and b/sphinx/_static/video_button.png differ diff --git a/sphinx/_templates/layout.html b/sphinx/_templates/layout.html index 4e53265..c262f01 100644 --- a/sphinx/_templates/layout.html +++ b/sphinx/_templates/layout.html @@ -2,68 +2,51 @@ {% block extrahead %} + + + + {% endblock %} -{% block rootrellink %} -
  • Debian || 
    • -
  • Neuroscience : 
    • -
  • Software | 
    • -
  • Datasets | 
    • -
  • Virtual Machine | 
    • -
  • FAQ | 
    • -
  • Testimonials  
    • +{% block header %} +
    + +
    +
    {% endblock %} +{% block rootrellink %}{% endblock %} + {% block relbaritems %}
  • Comments |
    • -{% endblock %} - -{% block sidebar1 %}{% endblock %} - -{% block sidebar2 %} -{{ sidebar() }} -{% endblock %} - {% block sidebarsearch %} {{ super() }} - -

    -

    - - - -
    -

    - - - -

    Click to get yourself listed as a NeuroDebian user

    -

    NITRC-listed

    +{% endblock %} +
    • +
  • {{ super() }} -
    +
    The source code for this portal is licensed under the GPL-3 and is available on @@ -71,5 +54,43 @@ The source code for this portal is licensed under the title="Browse or clone the Git repository"> git.debian.org.
    + + + + + + + + + {% endblock %} diff --git a/sphinx/_templates/searchbox.html b/sphinx/_templates/searchbox.html new file mode 100644 index 0000000..67f7717 --- /dev/null +++ b/sphinx/_templates/searchbox.html @@ -0,0 +1,10 @@ +{%- if pagename != "search" %} +
    • +{%- endif %} diff --git a/sphinx/blog/2010/index.rst b/sphinx/blog/2010/index.rst index 9faa409..2799be6 100644 --- a/sphinx/blog/2010/index.rst +++ b/sphinx/blog/2010/index.rst @@ -1,5 +1,5 @@ -2010 -==== +Blog posts in 2010 +================== .. toctree:: :maxdepth: 1 diff --git a/sphinx/blog/2011/index.rst b/sphinx/blog/2011/index.rst index 401c15f..0053072 100644 --- a/sphinx/blog/2011/index.rst +++ b/sphinx/blog/2011/index.rst @@ -1,5 +1,5 @@ -2011 -==== +Blog posts in 2011 +================== .. toctree:: :maxdepth: 1 diff --git a/sphinx/blog/2012/index.rst b/sphinx/blog/2012/index.rst index f1882a3..602f9cb 100644 --- a/sphinx/blog/2012/index.rst +++ b/sphinx/blog/2012/index.rst @@ -1,5 +1,5 @@ -2012 -==== +Blog posts in 2012 +================== .. toctree:: :maxdepth: 1 diff --git a/sphinx/coffeeart.rst b/sphinx/coffeeart.rst index e64b075..be8f8cf 100644 --- a/sphinx/coffeeart.rst +++ b/sphinx/coffeeart.rst @@ -195,4 +195,14 @@ Coffee Art .. figure:: /pics/coffeeart/IMG_6647.JPG +.. raw:: html + + diff --git a/sphinx/conf.py b/sphinx/conf.py index 226e940..3ae121a 100644 --- a/sphinx/conf.py +++ b/sphinx/conf.py @@ -64,7 +64,7 @@ master_doc = 'index' # General information about the project. project = u'Debian Neuroscience Package Repository' -copyright = u'2009-2011, NeuroDebian Team' +copyright = u'2009-2012, NeuroDebian Team ' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -118,6 +118,15 @@ pygments_style = 'sphinx' # given in html_static_path. html_style = 'neurodebian.css' +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +html_theme_options = {'nosidebar': True} + # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". html_title = project diff --git a/sphinx/dump.rst b/sphinx/dump.rst new file mode 100644 index 0000000..d7f76ba --- /dev/null +++ b/sphinx/dump.rst @@ -0,0 +1,118 @@ +.. _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 + +.. _chap_mailinglists: + +* 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. + +.. _chap_team: + +The team +======== + +`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 + + +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 + +.. _chap_popularity: + +Popularity +========== + +.. 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. + + diff --git a/sphinx/faq.rst b/sphinx/faq.rst index 4757eca..1249930 100644 --- a/sphinx/faq.rst +++ b/sphinx/faq.rst @@ -8,9 +8,11 @@ Frequently Asked Questions ************************** -Why NeuroDebian? ----------------- +.. raw:: html + +
    Click on an item to expand it
    +Why NeuroDebian? In the course of our own research endeavors |we| have joined forces to develop `PyMVPA -- a Python framework for multivariate pattern analysis of neural data `_. To conveniently deploy PyMVPA for @@ -23,13 +25,13 @@ Why NeuroDebian? Why is NeuroDebian not a Pure Blend? ------------------------------------- + This is in the works, but... - Because there is no need for it to become one, as the existing Debian Pure - Blends already offer the desired functionality *within* Debian. Similar to - Pure Blends, NeuroDebian's goal is to provide software for neuroscientists - using the Debian operating system, and therefore the ultimate goal is to get - all relevant software **into Debian**. + There is no need for it to become one, as the existing Debian Pure Blends + already offer the desired functionality *within* Debian. Similar to Pure + Blends, NeuroDebian's goal is to provide software for neuroscientists using + the Debian operating system, and therefore the ultimate goal is to get all + relevant software **into Debian**. However, various reasons exist that prevent a particular software from entering Debian. Some are temporary, i.e. a package is already useable, but @@ -54,8 +56,6 @@ Why is NeuroDebian not a Pure Blend? I want to help. How do I get involved? --------------------------------------- - We always need people to help maintaining existing packages. If you need some additional software packaged and you want to try it on your own, we would be happy to mentor you. We also have a :ref:`list of ongoing and planned @@ -66,8 +66,6 @@ I want to help. How do I get involved? When does a package migrate from NeuroDebian into Debian proper? ----------------------------------------------------------------- - In short: When it is ready. The longer answer is that there is nothing special to packages in NeuroDebian in comparison to packages conducted elsewhere. Packaging efforts are announced to Debian via ITPs_ and the @@ -86,8 +84,6 @@ When does a package migrate from NeuroDebian into Debian proper? Debian, Debian, Debian -- What about Ubuntu? --------------------------------------------- - NeuroDebian offers backported binary packages for recent Ubuntu releases whenever possible. However, since Ubuntu (like many other derivatives) uses Debian as its foundation, it is more efficient to spend time maintaining @@ -103,32 +99,26 @@ Debian, Debian, Debian -- What about Ubuntu? How to create a mirror of the repository? ------------------------------------------ - The NeuroDebian repository can be mirrored with rsync. If you are interested in sponsoring storage space and bandwidth for another mirror, please `contact us `_. How do I get a new neuroscience-related FOSS into (Neuro)Debian? ----------------------------------------------------------------- - -The goal of NeuroDebian is to package neuroscience software for Debian. Hence -getting software into NeuroDebian means trying to get it into Debian. There are -at least two possibilities to achieve that: + The goal of NeuroDebian is to package neuroscience software for Debian. Hence + getting software into NeuroDebian means trying to get it into Debian. There are + at least two possibilities to achieve that: -* You can approach packaging it yourself. Start by filing an ITP_ (Intent to - package) bugreport) and `ask us `_ to mentor your - upload to Debian_, if you are not a Debian developer. + * You can approach packaging it yourself. Start by filing an ITP_ (Intent to + package) bugreport) and `ask us `_ to mentor your + upload to Debian_, if you are not a Debian developer. -* `Contact us `_ -- but then it might take a little - longer, depending on our current workload and interest in a particular - software. + * `Contact us `_ -- but then it might take a little + longer, depending on our current workload and interest in a particular + software. I have heard that some packages are non-free. Will you charge me for them? --------------------------------------------------------------------------- - No. The term :term:`non-free` refers to an archive section. NeuroDebian uses exactly the same `archive sections as Debian proper `_. The *non-free* @@ -142,42 +132,38 @@ I have heard that some packages are non-free. Will you charge me for them? .. _sec_pkg_authentication: What means "The following signatures couldn't be verified..."? --------------------------------------------------------------- + When you start using this repository, you probably get warning messages + like this:: -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. - 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:: -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]? - 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. It is easy to + make APT happy again. The simplest way is to install the ``neurodebian-keyring`` + package that is available from the NeuroDebian repository. Alternatively: -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. The simplest way is to install the ``neurodebian-keyring`` -package that is available from the NeuroDebian repository. Alternatively: + 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). -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). + 2. Now feed the key into APT by invoking:: -2. Now feed the key into APT by invoking:: + apt-key add #file# - apt-key add #file# - - 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). + 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). How can I cite NeuroDebian? ---------------------------- - -Please cite the following paper: + Please cite the following paper: Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the next step: An integrated, community-driven computing platform for neuroscience diff --git a/sphinx/index.rst b/sphinx/index.rst index 979c028..718e1b7 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -1,28 +1,18 @@ .. _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 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>`_. -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 @@ -31,64 +21,63 @@ Please help us |spread|: .. raw:: html -

    - - - - - - - -

    +
    more publications
    +
    + +
    +
    -.. _Ubuntu: http://www.ubuntu.com +.. quotes:: + :random: 1 -.. _news: +.. raw:: html -News -==== +
    +
    more testimonials
    -.. raw:: html +.. _Ubuntu: http://www.ubuntu.com - -
    - +.. _repository_howto: +.. _chap_installation: -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. +Get NeuroDebian +=============== -.. _identi.ca: http://identi.ca/neurodebian -.. _twitter: http://twitter.com/NeuroDebian +First select what kind of operating system you are using, and then choose a +download server close to you: -.. _repository_howto: +.. include:: sources_lists +.. raw:: html +
    + This form requires javascript. If disabled, incomplete instructions are + displayed below
    +
    +
    + Instructions for Debian-derived systems +
    -How to use this repository -========================== +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. -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 + 
    +  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 @@ -97,234 +86,130 @@ the terminal you can use :command:`apt-get`:: .. raw:: html -

    +
    -Popularity Contest ------------------- +
    +
    + Instructions for non-Debian systems +
    -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:: +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: - sudo dpkg-reconfigure popularity-contest +1. Download this image file: + +.. raw:: html + + + +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). + +3. Finish the configuration by following :ref:`the instructions on setting up + the virtual appliance `. `[Virtual machine + setup video tutorial] `_ + + + + +You are ready to go -- enjoy NeuroDebian! .. 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:: + 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. - sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf - DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest + * `NeuroDebian 6.0.2 image (32bit) + `_ [~545MB] -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. + * `NeuroDebian 6.0.2 image (64bit) + `_ [~560MB] -.. _chap_installation: +.. raw:: html -Ways to use NeuroDebian -======================= +
    -Virtual machine ---------------- +.. _virtual appliance: http://en.wikipedia.org/wiki/Virtual_appliance +.. _VirtualBox: http://www.virtualbox.org -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. +.. _news: +News +==== -Debian installation -------------------- +.. raw:: html -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|. + +
    + +
    + The news widget requires javascript +
    +.. _identi.ca: http://identi.ca/neurodebian +.. _twitter: http://twitter.com/NeuroDebian -.. _chap_team: +.. raw:: html + +
    +
    -The team -======== +* **About** +* :ref:`Team ` +* :ref:`chap_popularity` +* :ref:`FAQ ` +* :ref:`Blog ` +* :ref:`chap_publications` +* :ref:`testimonials` +* :ref:`coffeeart` -`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. +.. start a new list -.. _maintainers: pkgs.html#by-maintainer +* **Services** +* :ref:`Software ` +* :ref:`Data ` +* :ref:`Appliance ` +.. start a new list -.. _support: - -Contacts -======== +* **Community** +* :ref:`Mailing lists ` +* `OpenHatch `_ +* `Identi.ca `_ +* `Twitter `_ +* `Google+ `_ +* `YouTube `_ +* `GitHub `_ -`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 +.. start a new list -* 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 `_] +* **Related** +* `Debian `_ +* `Debian Med `_ +* `INCF `_ +* `NITRC `_ + +.. raw:: html -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:: @@ -335,6 +220,7 @@ efficient, more open, and more fun pkgs spread vm + publications coffeeart photoalbum projects @@ -352,6 +238,110 @@ efficient, more open, and more fun quotes-nitrc sources_lists vm_welcome + dump .. include:: link_names.txt .. include:: substitutions.txt + +.. raw:: html + + diff --git a/sphinx/projects.rst b/sphinx/projects.rst index 8443483..b03d6c1 100644 --- a/sphinx/projects.rst +++ b/sphinx/projects.rst @@ -63,15 +63,18 @@ Expertise transfer Promotion --------- +.. raw:: html + +
    Click on an item to expand it
    + * `Publications `_ and promotional materials - - `Debian / NeuroDebian tri-fold + - `(Neuro)Debian tri-fold `_ * Conferences presence of the team presenting Debian_, NeuroDebian_, and related work: - **May 2-6, 2011** `Paradyn/Condor Week `_, Madison, Wisconsin, USA Hanke, M. `Talk: Integrating Condor into the Debian operating system `__ **June 26-30, 2011** `HBM 2011 `_, Québec City, Canada @@ -79,22 +82,21 @@ Promotion **July 21-23, 2011** `PsychoPy Workshop and Codesprint `_, New Haven, CT, USA **August 25-30, 2011** `EuroSciPy 2011/ Python in NeuroScience `_, Paris, France - 2011/08/27, 16:30 -- 17:00, Scientific track - Halchenko, Yaroslav O. `Talk: π's in Debian or Scientific Debian: NumPy, - SciPy and beyond `__ + Halchenko, Yaroslav O. `Talk: π's in Debian or Scientific Debian: NumPy, + SciPy and beyond `__ 2011/08/29, 14:00 -- 14:30, Neuroimaging data processing Halchenko, Yaroslav O. `Talk: The virtues and sins of PyMVPA `__ 2011/08/30, 10:30 -- 10:45, Workflows and pipelines for data processing Hanke, M. `Talk: More than batteries included: NeuroDebian `__ 2011/08/30, 12:00 -- 12:15, Data management and databasing - Hanke, M. `Talk: NiBabel: Conductor for a cacophony of neuro-imaging file formats `__ + Hanke, M. `Talk: NiBabel: Conductor for a cacophony of neuro-imaging file formats `__ **September 8, 2011** `INCF Cross-Task Force Hackathon `_, Boston, MA, USA **November 12-16, 2011** `SfN 2011 `_, Washington, District Columbia, USA Booth #3207 - `Invite us `_ +* `Invite us `_ to talk about NeuroDebian. * `Inviting contributions and new members to join the NeuroDebian project `_ diff --git a/sphinx/publications.rst b/sphinx/publications.rst new file mode 100644 index 0000000..b3469db --- /dev/null +++ b/sphinx/publications.rst @@ -0,0 +1,99 @@ + +.. _chap_publications: + +************ +Publications +************ + +This is a list of publication from the NeuroDebian team on various +NeuroDebian-related topics: + +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/ +.. _chap_popularity: + + diff --git a/sphinx/testimonials.rst b/sphinx/testimonials.rst index ec941a5..c93ad8c 100644 --- a/sphinx/testimonials.rst +++ b/sphinx/testimonials.rst @@ -3,6 +3,16 @@ Testimonials ============ +Here is some feedback we got from the neuroscience community on various +occasions. On this page it is grouped by its origin (i.e. `research +institutions`_, `research software projects`_, `individual laboratories and +researchers`_). Alternatively, you can read testimonials related to specific +topics: + +* :ref:`testimonials_open_science` +* :ref:`testimonials_standardization` +* :ref:`testimonials_vm` + .. None so far replied .. .. Organizations @@ -12,14 +22,6 @@ Testimonials .. :group: Organizations -By Topic --------- - -* :ref:`testimonials_open_science` -* :ref:`testimonials_standardization` -* :ref:`testimonials_vm` - - Research Institutions --------------------- diff --git a/sphinx/vm.rst b/sphinx/vm.rst index 8beca27..7a34c0e 100644 --- a/sphinx/vm.rst +++ b/sphinx/vm.rst @@ -3,16 +3,17 @@ NeuroDebian Virtual Machine =========================== +`Installation`_ | `Working with the virtual machine`_ | `Troubleshooting`_ | +`What has changed`_ + .. quotes:: :random: 1 :tags: vm -For those who are not yet running a Debian-based operation system we offer a -`virtual machine`_ that can be used with `VirtualBox`_, allowing users to benefit -from a Debian-based research environment on other operating systems. -This virtual machine initially comes as a compact Debian installation that can, -once installed, be equipped with a large variety of neuroscience software with -just a few mouse clicks (e.g. AFNI_, Caret_, FSL_, PyMVPA_). +For all systems running a non-Debian-based operation system, such as MS Windows +or Mac OS X, we offer a `virtual machine`_ that can be equipped with a large +variety of neuroscience software with just a few mouse clicks (e.g. AFNI_, +FSL_, PyMVPA_). .. _virtual machine: http://en.wikipedia.org/wiki/Virtual_machine .. _AFNI: http://afni.nimh.nih.gov/afni/ @@ -20,107 +21,24 @@ just a few mouse clicks (e.g. AFNI_, Caret_, FSL_, PyMVPA_). .. _FSL: http://www.fmrib.ox.ac.uk/fsl/ .. _PyMVPA: http://www.pymvpa.org - -Downloads ---------- - -* `NeuroDebian 6.0.6 image (32bit) - `_ [~559MB] - - *This image should work on virtually all systems that are supported by* - VirtualBox_ *and can be used whenever the, otherwise preferable, 64bit image - is not compatible with a host machine.* - -* `NeuroDebian 6.0.6 image (64bit) - `_ [~576MB] - - *This image only works on 64bit host machines with active hardware - virtualization support. The should include all recent Apple hardware and most - 64bit Windows systems.* - -Virtual appliances above carry guest additions for 4.x series of the -VirtualBox. If you still have VirtualBox 3.x, use previous 6.0.2 -virtual appliances: - -* `NeuroDebian 6.0.2 image (32bit) - `_ [~545MB] - -* `NeuroDebian 6.0.2 image (64bit) - `_ [~560MB] - -.. note:: - - This older virtual appliances are distributed as a `zip` file. Please - extract all files from the `.zip` file, using appropriate software - for your operating system. - -.. note:: - - You can verify that you have downloaded archives correctly using - `md5sums -c MD5SUMS - `_ . You can also verify - the authenticity of the `MD5SUMS - `_ itself using `gpg - --verify MD5SUMS.gpg - `_ signed with - NeuroDebian archive key. - -* `VirtualBox download page `_ (Windows, Linux, Mac, - Solaris) - - *This webpage offers installers of the VirtualBox application, as well as the - documentation.* - -Changes -------- - -6.0.6 -- 01 Oct 2012 - - * Updated core system to Debian squeeze 6.0.6 - -6.0.5 -- 10 Nov 2011 - - * Updated core system to Debian squeeze 6.0.3 - * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10 - - - ``~/host`` is now symlinked to correct path ``/media/sf_host`` - - ``brain`` user is added to ``vboxsf`` group so mounted host - directories should become readily available - - * Root partition size and swap space got doubled in size (40GB - and 2GB correspondingly). Space is allocated dynamically so - the actual size of the virtual drive should not grow unless - you use it - -6.0.4 -- 13 Jun 2011 - - * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4 - -6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4] - - * Updated to Debian squeeze 6.0.1 - * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org - * Appliance is available as a single file (.ova) ready for the import - -6.0.2 -- 08 Feb 2011 - -6.0.1 -- 01 Dec 2010 - -Documentation -------------- - The virtual machine contains an installation of `Debian 6.0 (squeeze)`_ with a GNOME_ desktop environment. All installed software comes from standard Debian -packages, or prospective Debian packages from NeuroDebian. This means that all -contained software is readily available for any system running a Debian -operating system (or a recent Ubuntu release). The virtual machine can be seen -as a showcase of what Debian for neuroscience research feels like. Moreover, -once downloaded this virtual machine can be kept up to date, just as any other +packages, or prospective Debian packages from NeuroDebian. The virtual machine +can be seen as a showcase of what Debian for neuroscience research feels like. +Once downloaded this virtual machine can be kept up to date, just as any other Debian installation. Using convenient graphical package management tools users will benefit from security bug fixes provided by the Debian project for the whole operating system, as well as from software updates for neuroscience-related packages. +Even on Debian-based systems this virtual machine is an excellent way to +maintain an analysis environment that remains identical throughout the lifetime +of a study and that can be archived alongside acquired data and publications. +This is a much more practical way than freezing the entire software stack of a +whole workstation, where it quickly becomes troublesome to combine the desire +for latest research methodology for new studies and the need for stability for +ongoing projects. + .. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze .. _GNOME: http://www.gnome.org/ @@ -128,31 +46,25 @@ neuroscience-related packages. Installation ~~~~~~~~~~~~ -The following video shows how to get the NeuroDebian virtual machine running -on your machine. The installation is shown for Mac OS X. It should, however, be -very similar on a Windows box. If you cannot watch the video, please take a -look at the written instructions below. - -.. raw:: html - - +The following instructions demonstrate how to install the NeuroDebian virtual +machine -- here shown exemplary for Mac OS X, but the procedure is virtually +identical on a Windows box. There is also a video tutorial at coffee break +length. `[Virtual machine setup video tutorial] +`_. -First download and install a recent version of VirtualBox_. VirtualBox is a -virtualization software that is freely available for Windows, MacOS X, Solaris, -and Linux. VirtualBox comes with a comprehensive manual that should answer -potential questions regarding installation and maintenance. +If you don't have t already, first download and install a recent version of +VirtualBox_. VirtualBox is a virtualization software that is freely available +for Windows, MacOS X, Solaris, and Linux. VirtualBox comes with a comprehensive +manual that should answer potential questions regarding installation and +maintenance. .. _VirtualBox: http://www.virtualbox.org -Next, download the most recent version of the NeuroDebian virtual machine from -the Downloads_ section. Start VirtualBox and select "Import Appliance" from the file -menu. +Obtain the most recent version of the NeuroDebian virtual machine by visiting +http://neuro.debian.net and selecting your operating system and a download +server on the frontpage. + +Start VirtualBox and select "Import Appliance" from the file menu. .. image:: pics/vm_import_app.jpg @@ -203,10 +115,15 @@ connection you can update the contained software packages at any time. .. image:: pics/vm_settings.jpg -The virtual machine logs yourself in automatically. The name of the virtual -machine user is `brain` and the password is `neurodebian`. The *root* password -is also `neurodebian`. In most cases, however, you should not be forced to type -the password, since `sudo` is configured to work without it. +The virtual machine logs yourself in automatically. This is the default account: + +:user: brain +:password: neurodebian + +:root password: neurodebian + +In most cases you should not be forced to type the password, because ``sudo`` +is configured to work without it. .. note:: @@ -217,20 +134,13 @@ the password, since `sudo` is configured to work without it. Working with the virtual machine ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -The next video is a demonstration of some basic desktop integration features. -It shows how to use the virtual machine in full-screen and seamless mode, shared -folder access, software installation, as well as suspending and resuming the -virtual machine. - -.. raw:: html - - +The NeuroDebian virtual machine has very low maintenance demands. We have +prepared a short video demo that shows most typical procedures that you will +probably perform while working with NeuroDebian inside a virtual machine: +use the virtual machine in full-screen and seamless mode, shared folder access, +software installation, as well as suspending and resuming the +virtual machine. `[Virtual machine handling video tutorial] +`_ .. _chap_vm_troubleshooting: @@ -238,8 +148,11 @@ virtual machine. Troubleshooting ~~~~~~~~~~~~~~~ -Updating the VM or installing new packages doesn't work. +.. raw:: html + +
    Click on an item to expand it
    +Updating the VM or installing new packages doesn't work The VM uses as service that tries to figure out the best/closest package repository for you. In some network environments this service might not work well, or not at all. To check if this is a problem, you can modify the @@ -260,8 +173,18 @@ Updating the VM or installing new packages doesn't work. Only modify lines that refer to ``geomirror`` (all of them), but do **not** modify entries for ``security.debian.org``. -I cannot hear sounds played in the virtual machine. +Our proxy setup at work prevents APT from downloading packages + APT needs to be told how to access the proxy. Talk to your local sysadmin + and ask for the proxy's address (maybe a username and password too), as well + as the ports for HTTP and FTP proxies. With this information add the following + lines in the file, /etc/apt/apt.conf.d/80proxy. This will ensure that after an + upgrade changes won't be lost:: + Acquire::http::proxy "http://:@:/"; + Acquire::ftp::proxy "ftp://:@:/"; + Acquire::https::proxy "https://:@:/"; + +I cannot hear sounds played in the virtual machine By default the sound is muted. To enable playback launch the mixer applet by clicking on the mixer icon in the task bar. Unmute the master volume control. Now click on the "Volume control" to load the channel mixer dialog. Unmute @@ -269,9 +192,7 @@ I cannot hear sounds played in the virtual machine. now be able to hear sounds played within the virtual machines through your host computer's speakers. -I have upgraded VirtualBox from 3.x series to 4.x, and my VM lost -mounted host directories. - +My VM lost mounted host directories after upgrading from VirtualBox from 3.x to 4.x NeuroDebian VMs prior 6.0.3 were shipped with guest additions from 3.x series of VirtualBox and some initial versions of VirtualBox in 4.x series have failed to mount host directories properly. @@ -285,3 +206,42 @@ mounted host directories. virtualbox-ose-guest-utils virtualbox-ose-guest-x11 and reboot VM. + + +What has changed +---------------- + +.. raw:: html + +
    Click on an item to expand it
    + +6.0.6 -- 01 Oct 2012 + + * Updated core system to Debian squeeze 6.0.6 + +6.0.5 -- 10 Nov 2011 + * Updated core system to Debian squeeze 6.0.3 + * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10 + + - ``~/host`` is now symlinked to correct path ``/media/sf_host`` + - ``brain`` user is added to ``vboxsf`` group so mounted host + directories should become readily available + + * Root partition size and swap space got doubled in size (40GB + and 2GB correspondingly). Space is allocated dynamically so + the actual size of the virtual drive should not grow unless + you use it + +6.0.4 -- 13 Jun 2011 + * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4 + +6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4] + * Updated to Squeeze 6.0.1 + * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org + * Appliance is available as a single file (.ova) ready for the import + +6.0.2 -- 08 Feb 2011 + * Minor update + +6.0.1 -- 01 Dec 2010 + * Minor update