Merge remote-tracking branch 'gh-neurodebian/master'

* gh-neurodebian/master:
  Add information about NEST live media

diff --git a/artwork/ndhackergotchi.svg b/artwork/ndhackergotchi.svg
new file mode 100644 (file)
index 0000000..faa4376
--- /dev/null
+++ b/artwork/ndhackergotchi.svg
@@ -0,0 +1,957 @@
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+       inkscape:connector-curvature="0" />
+    <path
+       style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#000000;stroke-width:3.77901149;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;stroke-dashoffset:0"
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+       style="fill:none;stroke:#000000;stroke-width:2.65748024;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
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+       id="path3538"
+       sodipodi:nodetypes="ccc"
+       inkscape:connector-curvature="0" />
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+</svg>

diff --git a/cmdsettings.sh b/cmdsettings.sh
index de162cae59bfecc7f16dfb0698635f9bceb8af92..7068e935af55fd8b528569a2513e3fc2b46961c2 100644 (file)
--- a/cmdsettings.sh
+++ b/cmdsettings.sh
@@ -7,7 +7,7 @@ buildplace="${cowbuilderroot}/build"
 
 # all currently supported dists
 allnddists="nd+debian-squeeze nd+debian-wheezy nd+debian-sid \
-            nd+ubuntu-hardy nd+ubuntu-karmic nd+ubuntu-lucid nd+ubuntu-maverick nd+ubuntu-natty nd+ubuntu-oneiric nd+ubuntu-precise nd+ubuntu-quantal"
+            nd+ubuntu-hardy nd+ubuntu-lucid nd+ubuntu-oneiric nd+ubuntu-precise nd+ubuntu-quantal"
 alldists="$allnddists debian-squeeze debian-wheezy debian-sid"
 
 # default is debian

diff --git a/neurodebian.cfg b/neurodebian.cfg
index 11cb63daf06d2058a3be6038eece610ec94402fa..8c6d8ee90e4fce14cacecb8cd49307b7855a3022 100644 (file)
--- a/neurodebian.cfg
+++ b/neurodebian.cfg
@@ -23,7 +23,7 @@ select names = libnifti2 odin mitools afni-atlases python-pyssdh python-networkx
  python-sklearn python-scikits-learn python-mdp python-mlpy python-openpyxl libgdf-dev matlab-support
  svgtune rorden-mri-tutorial caret-data python-joblib python-sphinx fail2ban
  python-pandas python-skimage neurodebian numdiff nuitka pytables
- guacamole freeipmi remake
+ guacamole freeipmi remake vowpal-wabbit
 
 # Information about prospective packages to be imported from taskfiles
 prospective =

diff --git a/sphinx/quotes-nihr01.rst b/sphinx/quotes-nihr01.rst
index c7b57f53520a23f9997478e5b680a52c640b573f..dcfc0742f56c63ac92711740c8dea502b09c56a4 100644 (file)
--- a/sphinx/quotes-nihr01.rst
+++ b/sphinx/quotes-nihr01.rst
@@ -124,7 +124,8 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Prof. Brian Avants
    :affiliation: Research Assistant Professor of Radiology, University of Pennsylvania, Philadelphia, USA
    :date: 2010-09-16
-   :tags:  lofs, practices, standardization, mentorship, dissemination, impact
+   :tags:  lofs, practices, standardization, mentorship,
+                  dissemination, impact, upstream
    :group: Research software projects
 
    The NeuroDebian team taught me a great deal about how to systematize software development for reliable dissemination [...] This speaks very highly of the deep skillset and commitment to user support represented in the NeuroDebian project, which will have high impact on the field and help standardize both the analysis and the interpretation of neuroimaging data.
@@ -134,7 +135,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Dr. Matthew Brett
    :affiliation: Specialist researcher, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
    :date: 2010-09-02
-   :tags:  lofs, practices, team, sharing
+   :tags:  lofs, practices, team, sharing, upstream
    :group: Research software projects
 
    [...] your team are ideally placed to make this system work. I have worked with Yaroslav Halchenko and Michael Hanke.  [...] Their record on working together as a team, and individually, is easy to find, and speaks for itself.  Their demonstrated combination of seemingly inexhaustible energy, openness and skill has been of enormous benefit to our own project and community.  
@@ -144,7 +145,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Prof. Gene Cooperman
    :affiliation: College of Computer and Information Science, Northeastern University, Boston, USA
    :date: 2011-06-21
-   :tags:  lofs
+   :tags:  lofs, upstream
    :group: Research software projects
 
    [...] we have benefited from the NeuroDebian team through their mentoring and direct efforts to improve the DMTCP software for wider distribution.
@@ -154,7 +155,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Sebastian Eichelbaum
    :affiliation: OpenWalnut project, Image and Signal Processing Group, Institute of Computer Science, University of Leipzig, Germany
    :date: 2011-06-30
-   :tags:  lofs, mentorship
+   :tags:  lofs, mentorship, upstream
    :group: Research software projects
 
    We are currently preparing our first software-release in NeuroDebian and found it to be easy and straight-forward with a great support.
@@ -164,7 +165,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Prof. Bruce Fischl
    :affiliation: Director, Computational Core at Martinos Center at Massachusetts General Hospital, Charlestown, Massachusetts, USA
    :date: 2010-09-10
-   :tags:  lofs, perspective, software distribution
+   :tags:  lofs, perspective, software distribution, upstream
    :group: Research software projects
 
    Having FreeSurfer integrated into the Debian operating system by the NeuroDebian team would have enormous benefits for us, and for the thousands of users of FreeSurfer across the world.
@@ -174,7 +175,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Stephan Gerhard
    :affiliation: Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
    :date: 2011-06-21
-   :tags:  lofs, support, Debian, open science
+   :tags:  lofs, support, Debian, open science, upstream
    :group: Research software projects
 
    The Debian project provides the scientific community with a truly universal operating system. The breadth and quality of its community-driven development and technical support is superior to many other available commercial alternatives. It provides a sound basis for the open science movement.
@@ -184,7 +185,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Dr. Satrajit Ghosh
    :affiliation: Research scientist, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    :date: 2011-06-13
-   :tags:  lofs, software distribution
+   :tags:  lofs, software distribution, upstream
    :group: Research software projects
 
    In creating a source repository for distribution of common neuroimaging tools, NeuroDebian has filled a gaping void. It is an incredibly useful resource that we have been relying on at MIT for installation of software.
@@ -194,7 +195,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Valentin Haenel
    :affiliation: Psignifit and pyoptical developer, Modellierung Kognitiver Prozesse, Technische Universität, Berlin, Germany
    :date: 2010-09-17
-   :tags:  lofs, reproducibility
+   :tags:  lofs, reproducibility, upstream
    :group: Research software projects
 
    [ [...] The] only way to conduct reliable and reproducible science is to use open source software [...]. NeuroDebian is by far the most advanced undertaking for such a scientific approach in the neuroscience community.
@@ -204,7 +205,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Dr. Thies Jochimsen
    :affiliation: Post-doctoral researcher, Medical Physics Group, Department of Diagnostic and Interventional Radiology, University Hospital Jena, Jena, Germany
    :date: 2010-09-02
-   :tags:  lofs, team, software distribution, mentorship
+   :tags:  lofs, team, software distribution, mentorship, upstream
    :group: Research software projects
 
    [...] distributing the software via NeuroDebian generates valuable feedback which is indispensable for the development of free software. When working with the NeuroDebian team in the past, I have found their members to be very cooperative,    target-oriented and responsive.
@@ -214,7 +215,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Mario Kleiner
    :affiliation: Dipl. Inf., Psychtoolbox lead developer, Department for Cognitive and Computational Psychophysics, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
    :date: 2011-06-21
-   :tags:  lofs, vm, contributions, practices
+   :tags:  lofs, vm, contributions, practices, upstream
    :group: Research software projects
 
    We find the approach taken by NeuroDebian and the progress it made so far very pleasant and promising.  [...] The NeuroDebian team helped us to improve the quality of our software and of some of our processes by review, constructive suggestions and even software patches.  The availability of the NeuroDebian Virtual Machine was instrumental for fast porting of the Psychtoolbox to a 64 bit Linux environment.
@@ -224,7 +225,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Dr. Gabriele Lohmann
    :affiliation: Lipsia lead developer, Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
    :date: 2010-09-13
-   :tags:  lofs
+   :tags:  lofs, upstream
    :group: Research software projects
 
    It [NeuroDebian] has been and continues to be of great value in all of our projects [...]
@@ -234,7 +235,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Valerio Lucio
    :affiliation:  Manager Information Systems, Center for Brain Imaging, New York University, New York City, USA
    :date: 2010-09-01
-   :tags:  lofs, contributions, Debian
+   :tags:  lofs, contributions, Debian, upstream
    :group: Research software projects
 
    The dinifti tool was one of the first to appear in Debian and ever since it's inclusion in the distribution, I have received invaluable feedback from the Debian community 
@@ -244,7 +245,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Sebastiaan Mathôt
    :affiliation: OpenSesame lead developer, Vrije Universiteit, Amsterdam, The Netherlands
    :date: 2011-07-29
-   :tags:  lofs, software distribution, mentorship, Debian
+   :tags:  lofs, software distribution, mentorship, Debian, upstream
    :group: Research software projects
 
    The NeuroDebian team has helped me to make my software (OpenSesame) available to the wider public in a much more professional fashion than I would have been able to do for myself.
@@ -254,7 +255,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Dr. Eilif Muller
    :affiliation: Post-doctoral researcher, Brain Mind Institute, EPFL, Lausanne, Switzerland
    :date: 2010-09-09
-   :tags:  lofs, reproducibility, standardization, breadth
+   :tags:  lofs, reproducibility, standardization, breadth, upstream
    :group: Research software projects
 
    I am constantly aware that software packaging and supporting user needs on diverse platforms represents a severe burden for developers. The NeuroDebian software platform addresses these problems for a good fraction of production environments in the field, while contributing to research reproducibility through software standardization.  
@@ -264,7 +265,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Prof. Jonathan Peirce
    :affiliation: School of Psychology, University of Nottingham, Nottingham, UK
    :date: 2010-09-06
-   :tags:  lofs, money, impact
+   :tags:  lofs, money, impact, upstream
    :group: Research software projects
 
    Having such a group of experts [NeuroDebian developers] that search for open-source software solutions, refine them and then make them trivially easy for users to install and try out is of absolutely invaluable benefit to the research community and to the funding bodies that would, otherwise, be paying much larger sums in commercial software licensing fees.
@@ -274,7 +275,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Dr. Fernando Perez
    :affiliation: IPython developer, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
    :date: 2010-09-08
-   :tags:  lofs, contributions, team
+   :tags:  lofs, contributions, team, upstream
    :group: Research software projects
 
    Their [NeuroDebian developers] commitment to strongly tested, validated and documented tools for computational-based research in neuroscience is exemplary, and we owe them a great debt of gratitude for the contributions they have already made [...]
@@ -284,7 +285,8 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Dr. Ariel Rokem
    :affiliation: NiTime developer, Helen Wills Neuroscience Institute, University of California, Berkeley, USA
    :date: 2010-09-15
-   :tags:  lofs, frontier, contributions, speed, standardization, dissemination
+   :tags:  lofs, frontier, contributions, speed, standardization,
+                  dissemination, upstream
    :group: Research software projects
 
    NeuroDebian is playing a key role in the creation of an ``eco-system'' of open-source solutions for neuroscience  [...] The standards and practices disseminated by the NeuroDebian project allowed me to start using this tool [PsychoPy] efficiently and rapidly and to contribute back to the project within a few months.
@@ -294,7 +296,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Prof. Per B. Sederberg
    :affiliation: Department of Psychology, Ohio State University, Columbus, Ohio, USA
    :date: 2010-09-16
-   :tags:  lofs, impact, quality
+   :tags:  lofs, impact, quality, upstream
    :group: Research software projects
 
    [...] NeuroDebian will undoubtedly have a large impact on the quality of neuroscience research, both directly and indirectly, by making almost every known software package related to neuroscience work available in a stable and secure environment and broadening the standard set of techniques researchers can employ. 
@@ -304,7 +306,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Prof. Stephen M. Smith
    :affiliation: Associate Director, Centre for Functional Magnetic, Resonance Imaging of the Brain University of Oxford, Oxford, UK
    :date: 2010-09-01
-   :tags:  lofs, contributions, support, Debian
+   :tags:  lofs, contributions, support, Debian, upstream
    :group: Research software projects
 
    Since 2007 we completely rely on the NeuroDebian project to provide users of the Debian/Ubuntu platform with FSL software packages and corresponding technical support.  [...] we have received a continuous stream of bug fixes and improvements that have been developed by members of the Debian community.  [...] we were able to benefit from work of people that would not otherwise contribute to the development of FSL – without any additional investment of my lab, but solely due to FSL’s presence in the Debian archive.  
@@ -314,7 +316,7 @@ Quotes from NIH R01 grant proposal letters of recommendation
    :author: Dr. Gaël Varoquaux
    :affiliation: Parietal project, INRIA, Neurospin research center, Gif sur Yvette, France
    :date: 2010-09-01
-   :tags:  lofs, reproducibility, dissemination
+   :tags:  lofs, reproducibility, dissemination, upstream
    :group: Research software projects
 
    The availability of a common platform [NeuroDebian] for many different neuroimaging software solutions makes it much easier to compare solutions and pick the tool of choice for a given research problem.

diff --git a/sphinx/quotes-nitrc.rst b/sphinx/quotes-nitrc.rst
index 7c641ff8ad4c218559cc25b75197eda0fadb86b6..00c1e529457b035d584639d1c0cb68ff6b57489c 100644 (file)
--- a/sphinx/quotes-nitrc.rst
+++ b/sphinx/quotes-nitrc.rst
@@ -21,11 +21,13 @@ Quotes from NITRC project page
 
    [...] Best part for me is that I can run it in a VM without having to worry about replacing my native OS.
 
+
 .. quote::
-   :author: Robert Buccigrossi
+   :author: Dr. Robert Buccigrossi
+   :affiliation: Technical Lead of the NITRC project
    :date: 2011-09-22
    :tags: nitrc, ease
-   :group: Individual laboratories and researchers
+   :group: Research software projects
    :source: NITRC forum: http://www.nitrc.org/forum/message.php?msg_id=5013
 
    Dr. Halchenko's statement "Discover http://neuro.debian.net and be happy" may sound a bit like a sales pitch, but it is rather good advice.  We have been experimenting with the rapid instantiation of computational environments containing neuroimaging tools from NITRC, and the NeuroDebian repository makes installing and updating the tools through apt-related package managers rather trivial.

diff --git a/sphinx/testimonials.rst b/sphinx/testimonials.rst
index ec941a5d393a77f8e78db0ba0803dde0f951b936..50ff648e31a44f7c6b4f3c159d70d81c0f2212c4 100644 (file)
--- a/sphinx/testimonials.rst
+++ b/sphinx/testimonials.rst
@@ -44,6 +44,84 @@ Research Software Projects
 
    For proper software packaging and distribution, the NeuroDebian project provides professional expertise and infrastructure.
 
+.. quote::
+   :author: Chuck Theobald
+   :affiliation: Lewis Center for Neuroimaging, University of Oregon, MRIConvert/mcverter build master and developer
+   :tags: email, impact, software distribution, upstream, dissemination
+   :date: 2013-02-06
+
+   As a system administrator, I support the efforts of a number of
+   researchers who use fMRI analysis software. I was overjoyed to find
+   the NeuroDebian repository, a one-stop shop for nearly every
+   software package the researchers use. The work of the NeuroDebian
+   Team greatly simplifies the task of providing our researchers the
+   best software available, and I consider the repository a vital part
+   of my professional life.  As a maintainer on the MRIConvert
+   project, I find that NeuroDebian provides a valuable venue for
+   dissemination of our software. It would not be possible to reach
+   the same wide audience without the NeuroDebian repository.
+
+.. quote::
+    :author: Dr. Kiyotaka Nemoto
+    :affiliation: University of Tsukuba
+    :tags: email, derivatives, time
+    :date: 2013-02-06
+
+    Neurodebian is the best solution for researchers in neuroscience.
+    Everybody should have experienced wasting so much time in just setting
+    up software. With Neurodebian repository, you can easily setup many
+    useful software packages and focus on your research. I recommend this
+    repository to everyone who is interested in using Linux in
+    neuroscience.
+
+.. quote::
+    :author: Dr. Andrew Janke
+    :affiliation: Center for Advanced Imaging, University of Queensland, Australia
+    :date: 2013-02-06
+    :tags: email, upstream, stability, versioning, provenance, vm,
+                  reproducibility, collaboration
+
+    We use NeuroDebian on a daily basis as it provides a stable and
+    versioned software base for analysis. This is critical as it allows us
+    to maintain data provenance, something that is often sorely lacking.
+    Our collaborators who don't quite have their heads around Linux yet
+    are pointed to the NeuroDebian Virtual Machine, it allows them to run
+    an identical analysis environment to us regardless of where they are
+    or operating system.
+
+.. quote::
+    :author: Christian Haselgrove
+    :affiliation: University of Massachusetts Medical School
+    :date: 2013-02-06
+    :tags: email, derivatives, management
+
+    Developing informatics infrastructure often involves building
+    complex systems that require interaction between existing
+    components such as software and atlases.  NeuroDebian makes it
+    trivial to manage the components of these systems, freeing me to
+    focus on the novel and important aspects of my work.
+
+.. quote::
+   :author: Nina Preuss
+   :affiliation: PMP, nitrc.org
+   :date: 2013-02-06
+   :tags: disqus, money, quality, contributions
+
+    NITRC-CE, or the NITRC Computational Environment, on the Amazon
+    Marketplace wouldn't have happened as quickly and thus cost effectively
+    without leveraging NeuroDebian's good works. We appreciative their
+    critical contribution to the neuroimaging compute community.
+
+.. quote::
+   :author: Sebastiaan Mathôt
+   :affiliation: Aix-Marseille université, Laboratoire de Psychologie Cognitive
+   :date: 2013-02-06
+   :tags: email, impact
+
+   For any neuroscientist that relies on open-source software,
+   NeuroDebian is the single most important resource.
+
+
 
 Individual Laboratories and Researchers
 ---------------------------------------
@@ -72,3 +150,28 @@ Individual Laboratories and Researchers
    VirtualBox, ran AFNI, and generated the files I needed, all within
    about an hour and a half. [...] not bad, considering that I know
    essentially no Linux/Unix. So here's a big "thanks!" :)
+
+.. quote::
+  :author: Vincent Kersten
+  :affiliation: University Medical Center Utrecht
+  :tags: email, standardization, money, Debian
+  :date: 2013-02-06
+
+  Neurodebian provides us with a consitent way of sotware packaging
+  and upgrades, eliminating tedious compiles and home-brew setups,
+  while seamlessly integrating with the Debian distribution. Excellent
+  and very valuable work, saving costs and difficult to spot
+  errors. High five Michael, Yaroslav and team! Keep them packages
+  coming!
+
+.. quote::
+   :author: Christian Stephan-Otto
+   :affiliation: Neuroimaging Research Group, Parc Sanitari Sant Joan de Deu, Barcelona, Spain
+   :date: 2013-02-06
+   :tags: email, vm, breadth
+
+   Since I started using a NeuroDebian virtual machine on win64 months
+   ago I am relying more and more on its diverse tools, from
+   population-specific template creation to pipelining the analysis of
+   fMRI, DTI and morphology studies. There is a great chance I will
+   end up working exclusively with NeuroDebian!