Merge branch 'master' of alioth:/git/pkg-exppsy/neurodebian

* 'master' of alioth:/git/pkg-exppsy/neurodebian:
  changes in vm.rst for 6.0.4
  VM BF: deploy 4.x VB -guest-utils and -guest-x11 in the appliance -- aiming at 6.0.4 now
  updated VM page for 6.0.3 virtual appliance
  VM: uff -- nasty workaround to get VB guest additions be built for 686
  VM: changes for 6.0.3
  VM: adjusting path to new location for source lists
  prepare VM images for VB 4.x series using squeeze-backports
  minor in proj_matlab -- moved finished into Done
  some updates into freesurfer project page

diff --git a/future/blends/debruijn b/future/blends/debruijn
new file mode 100644 (file)
index 0000000..5a94722
--- /dev/null
+++ b/future/blends/debruijn
@@ -0,0 +1,24 @@
+Source: debruijn
+Tasks: debian-science/psychophysics, debian-science/neuroscience-cognitive
+Homepage: http://www.cfn.upenn.edu/aguirre/wiki/public:de_bruijn_software
+Language: C++
+License: BSD (4-clause)
+Version: 1.3
+Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/debruijn.git
+Vcs-Git: git://git.debian.org/git/pkg-exppsy/debruijn.git
+Pkg-Description: De Bruijn cycle generator
+ Continuous carry-over, fMRI experiments present stimuli in a counter-balanced
+ sequence, meaning every stimulus precedes and follows every other. Higher
+ level counterbalancing is useful to guard against some modeling assumptions
+ of the approach and to test for the effects of stimulus history and context.
+ Sequences that efficiently provide this control of stimulus order are called
+ de Bruijn cycles.
+ .
+ This package provides a commandline tool to generate de Bruijn cycles.
+Pkg-URL: http://neuro.debian.net/pkgs/debruijn.html
+Published-Title: de Bruijn cycles for neural decoding
+Published-Authors: GK Aguirre, MG Mattar, L Magis-Weinberg
+Published-In: NeuroImage 56: 1293-1300
+Published-Year: 2011
+Published-DOI: 10.1016/j.neuroimage.2011.02.005
+Responsible: NeuroDebian Team <team@neuro.debian.net>

diff --git a/sphinx/_static/neurodebian.css b/sphinx/_static/neurodebian.css
index f20f4e9abffa3692f8bf324cac2c6f61bd36c607..19fd8cfcbb7fee965f6d16bc6d50a90a6da3e44a 100644 (file)
--- a/sphinx/_static/neurodebian.css
+++ b/sphinx/_static/neurodebian.css
@@ -684,6 +684,10 @@ img.logo {
     border: 0;
 }
 
+ol.loweralpha {
+    list-style: lower-alpha;
+}
+
 
 /* Epigraphs */
 
@@ -739,3 +743,44 @@ p.attribution span.affiliation, span.source {
         display: none;
     }
 }
+
+/* survey */
+
+
+div.rating {
+    text-align: center;
+    font-size: 80%;
+    float: left;
+    padding: 0.5em;
+}
+
+
+table.questionaire {
+    padding: 0px;
+}
+
+tr.oddrow {
+    background-color: #ddd;
+}
+
+table.questionaire td {
+    padding: 0px;
+    margin: 0px;
+}
+
+td.response {
+    text-align: left;
+    white-space: nowrap;
+    background-color: #eeffcc;
+}
+
+tr.oddrow td.response {
+    background-color: #ccd9af;
+}
+
+td.task {
+    text-align: left;
+}
+
+
+

diff --git a/sphinx/blog/2011/2011-06-15_letter_of_support.rst b/sphinx/blog/2011/2011-06-15_letter_of_support.rst
new file mode 100644 (file)
index 0000000..8ec1dd5
--- /dev/null
+++ b/sphinx/blog/2011/2011-06-15_letter_of_support.rst
@@ -0,0 +1,203 @@
+:date: 2011-06-15 10:00:00
+:tags: neuroscience, grant
+
+NeuroDebian needs your support
+==============================
+
+The NeuroDebian Team is asking for your support.  We are hoping to obtain
+funding for continued maintenance, development and expansion of the project.
+An initial grant proposal has already been reviewed and we are about to
+resubmit to address reviewer comments (PI `Dr. James V. Haxby`_; NIH program
+announcement PAR-08-010_: Continued Development and Maintenance of Software
+(R01)).
+
+.. _Dr. James V. Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
+.. _PAR-08-010: http://grants.nih.gov/grants/guide/pa-files/par-08-010.html
+
+Please see the abstract and specific aims at the end for a more
+detailed description of the updated project proposal.
+
+We need to address two main reviewer concerns:
+
+1. **Proof of the state of the project**
+
+   We previously failed to convince the reviewers that our efforts
+   **already** help researchers to maintain a productive research
+   software environment with minimal effort.  Therefore, if you are
+   using NeuroDebian, and you feel that it is beneficial for your
+   research activities, we would appreciate your letter of support
+   describing: Why did you start using NeuroDebian? What do you use it
+   for?
+
+2. **Feasibility of virtual environments for software deployment**
+
+   The reviewers argued that using a virtual environment (i.e. a virtual
+   machine, VM) is not a feasible solution to the problem of deploying an
+   integrated platform, like NeuroDebian, on the two major non-GNU/Linux
+   operating systems (Windows and Mac OS). Therefore, we would appreciate your
+   letter of support, if you rely on a VM to run or evaluate research software.
+   Such letter would preferably describe why you use a VM, and could offer a
+   short summary of the VM experience in your research activities.
+
+We also appreciate letters on other aspects of the proposal, and would be
+delighted to see requests for any particular functionality included in them.
+
+If you would like to see the NeuroDebian project to continue its development,
+we would be thankful if you send your "Letter of Support" via email_
+(preferably a PDF) or fax (+1 (603) 646-1419) to provide additional weight for
+our application.  For your convenience, we have composed a generic `letter
+template`_.
+
+.. _email: team@neuro.debian.net
+.. _letter template: http://neuro.debian.net/_files/letter_of_support_template.txt
+
+If you have previously provided us a letter of support, and either
+want to retract or alter it, based on the updated project description,
+please email us.
+
+We would appreciate if we receive your letter of support within a
+week, so we are still on time with the resubmission and ready to
+dedicate ourselves to HBM 2011 (visit us at booth #108).
+
+Thank you very much in advance for your support,
+
+the NeuroDebian team
+
+
+Proposal Abstract
+-----------------
+
+Complex software systems play a more and more important role in neuroscience
+research and managing an appropriate research environment is becoming
+increasingly difficult. `NeuroDebian <http://neuro.debian.net>`_ is a turnkey
+research software platform for all aspects of the neuroscientific research
+process. It takes the ideas of the Neuroimaging Tools and Resources
+Clearinghouse (`NITRC <http://www.nitrc.org>`_, on maximizing research
+transparency and methods sharing, one step further, by providing a
+comprehensive suite of readily usable and fully integrated software with a
+robust testing and deployment infrastructure. Consequently, it improves
+interoperability among the tools and frees researchers from the burden of
+tedious installation or upgrade procedures. That, in turn, positively affects
+their availability for actual research activities, as well as their motivation
+to test new analysis tools and stay connected with the latest methodological
+developments in the field.
+
+Over the past six years, NeuroDebian has integrated dozens of neuroscience
+software tools into the `Debian operating system <http://www.debian.org>`_,
+making its current version, Debian 6.0, the first operating system world-wide
+with comprehensive built-in support for MRI-based neuro-imaging research. In
+close collaboration with the Debian community and all involved neuroscience
+research groups we have provided middleware support for users and developers –
+consulting developers regarding release practices and legal aspects and
+streamlining technical support of NeuroDebian users. This joint effort has been
+well received by the research community, and, according to a recent survey,
+GNU/Linux-based systems are now the most common computing platform in
+neuroscience, and NeuroDebian is the most popular software resource dedicated
+to neuroscience.
+
+To further contribute to the dissemination of new methods, the NeuroDebian
+project aims to expand its coverage of software and to assure robust operation
+across a wide variety of deployment scenarios. Developing an environment with a
+large number of tightly integrated neuroscience software tools will allow for
+testing efforts that continuously verify software interoperability. We will
+develop a framework to derive a comprehensive description of a NeuroDebian
+analysis environment, and offer anyone the building blocks to, later on,
+reincarnate an identical copy, thus addressing an essential aspect of
+reproducible research. By means of virtualization solutions we will offer
+researchers the tools to take advantage of NeuroDebian on non-GNU/Linux
+operating systems, and advanced computing platforms (e.g., distributed and
+cloud computing) for efficient large-scale data analysis and modeling.
+
+By fostering proven and efficient practices of the free and open-source
+software community in neuroscience, NeuroDebian will help to assure the
+availability and continued usefulness of existing software.
+
+
+Specific aims
+-------------
+
+This project aims to further improve integration of neuroscience
+software into the larger free and open source software community by
+adopting standards and practices that have proven to yield a maximum
+of quality and productivity. To this end, we will keep working closely
+with a large number of neuroscience software developers, as well as
+the Debian community. In particular we aim to achieve:
+
+Aim 1: Ongoing maintenance of neuroscientific software in (Neuro)Debian
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+NeuroDebian currently maintains over 30 software projects, from
+single-purpose tools to complex analysis suites. All integrated
+software requires timely response to bug reports, and software
+updates. We aim to continue to offer reliable and prompt service in
+providing an efficient research environment.
+
+Aim 2: Increased coverage of neuroscientific research tools
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+To enhance the utility of NeuroDebian for a wide range of research
+applications we will
+
+a) extend software coverage beyond (f)MRI/DTI-based neuroimaging to
+   tools for intra/extra-cellular recording and modeling, EEG/MEG,
+   and data management: e.g., BrainVisa/Anatomist, Camino, DTI-TK,
+   FreeSurfer, NEURON, XNAT, and other software that becomes
+   available during the project lifetime;
+b) integrate essential Matlab-based open-source software: e.g.,
+   BrainStorm, EEGLAB, Fieldtrip, PsychToolbox, SPM;
+c) facilitate work on increasing the compatibility of Matlab-based
+   neuroscience tools with alternative open-source computing
+   platforms – such as Octave – to improve their availability in
+   high-throughput, and cloud computing environments and loosen
+   dependencies on proprietary systems;
+d) mentor interested developers in maintaining their software in
+   Debian by themselves.
+
+Aim 3: Quality and interoperability assurance
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Independent research software tools evolve at their own pace. This
+poses a challenge for heterogeneous computing environments. To
+assure reliability and interoperability without stagnation we will
+
+a) exercise available test batteries on recent and upcoming releases
+   of Debian and Ubuntu to assure robust performance and inform
+   developers about upcoming changes before researchers are affected;
+b) develop new test suites for common heterogeneous analysis
+   pipelines and run them routinely to assure proper functioning and
+   ongoing compatibility of all involved tools;
+c) make developed test suites readily available to users so they can
+   verify correct operation of their particular research
+   environments.
+
+Aim 4: Sustained availability of software and precise re-creation of complete research environments
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The scientific workflow frequently requires re-analyses of data with
+particular versions of software, for example, to revise a manuscript
+or to reproduce a study. We will
+
+a) employ Debian’s existing software archive snapshotting framework
+   to preserve and distribute all previous and current versions of
+   supported software in NeuroDebian;
+b) build on Debian’s package management systems, to develop tools to
+   describe a particular analysis environment (with all versioned
+   dependencies) to be able to reconstruct it at any later point in
+   time – by anyone – given access to the specification and to the
+   software archive snapshots.
+
+Aim 5: Broad availability of NeuroDebian on common and advanced computing platforms
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+A NeuroDebian-based system is not bound to computers solely running
+Debian. We will
+
+a) provide binary packages for Debian-derived operating systems
+   (e.g., Ubuntu);
+b) provide a virtual appliance allowing deployment of NeuroDebian in
+   a virtualized environment on proprietary operating systems
+   (e.g., Microsoft Windows and Mac OS X), as well as on other
+   non-Debian GNU/Linux distributions;
+c) provide NeuroDebian system images for cloud and high-throughput
+   computing that are compatible with popular service providers and
+   environments, such as Amazon EC2, and Condor.

diff --git a/sphinx/blog/2011/index.rst b/sphinx/blog/2011/index.rst
new file mode 100644 (file)
index 0000000..401c15f
--- /dev/null
+++ b/sphinx/blog/2011/index.rst
@@ -0,0 +1,9 @@
+2011
+====
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   2011*
+

diff --git a/sphinx/blog/2011/pics b/sphinx/blog/2011/pics
new file mode 120000 (symlink)
index 0000000..1bbd53b
--- /dev/null
+++ b/sphinx/blog/2011/pics
@@ -0,0 +1 @@
+../../pics
\ No newline at end of file

diff --git a/sphinx/blog/index.rst b/sphinx/blog/index.rst
index faabef31593428c56bb0efe03d0f83d3db03c76a..c3d78faa6b75310f7a82080ac138da7e8d19e811 100644 (file)
--- a/sphinx/blog/index.rst
+++ b/sphinx/blog/index.rst
@@ -7,3 +7,4 @@
    :glob:
 
    2010/index
+   2011/index

diff --git a/sphinx/index.rst b/sphinx/index.rst
index 84686326fb1729f857eb53d347c54d1e7dcaf7c1..558cedab712e9060f1409054b4c0071999d0f7bd 100644 (file)
--- a/sphinx/index.rst
+++ b/sphinx/index.rst
@@ -44,7 +44,7 @@ News
 .. raw:: html
 
  <script src="_static/jquery.livetwitter.min.js"></script>
- <div id="identica_widget"></div>
+ <div id="identica_widget">[imagine news items here]</div>
  <script type="text/javascript">
  $("#identica_widget").liveTwitter('neurodebian',
                                    {service: 'identi.ca',

diff --git a/survey/makestats b/survey/makestats
index 6dcd20ff2c08f80170adcc0d7e4feae52d10b2ec..c67a3ad72cca630a895c8eab704c6897ff551e20 100755 (executable)
--- a/survey/makestats
+++ b/survey/makestats
@@ -161,13 +161,18 @@ class DB(dict):
                 missing += 1
         return val, missing
 
-    def get_counts(self, key):
+    def get_counts(self, key, predef_keys=None):
         # return a dict with field values as keys and respective submission 
         # count as value
         vals = self.get_not_none(key)[0]
         uniq = np.unique(vals)
         counts = dict(zip(uniq, [vals.count(u) for u in uniq]))
-        return counts
+        if not predef_keys is None:
+            ret = dict(zip(predef_keys, [0] * len(predef_keys)))
+        else:
+            ret = {}
+        ret.update(counts)
+        return ret
 
     def select_match(self, key, values):
         # return a db with all submissions were a field id has one of the

diff --git a/survey/postprocdata b/survey/postprocdata
index abd834f6369a2ad36823d9f5be76179f1b0ac434..015e6b9d371b393af285073f009c06e11f4808ae 100755 (executable)
--- a/survey/postprocdata
+++ b/survey/postprocdata
@@ -149,6 +149,8 @@ for f in infiles:
             for v in values:
                 unhandled[v] = unhandled.get(v, 0) + 1
     verbose(3, "Storing file %s" % fname)
+    # shorten IP
+    j['remote_addr'] = '.'.join(j['remote_addr'].split('.')[:2]) + '.x.x'
     json.dump(j, open(os.path.join(dataout, fname), 'w'), indent=2)
     #open(os.path.join(dataout, fname), 'w').write(json.write(j))