\ndsubsection{Software at your fingertips}
\begin{flushright}
-\vspace{-0.5em}
+\vspace{-1em}
\url{http://neuro.debian.net/pkgs.html}
\end{flushright}
-\textit{Electrophysiology:} BioSig, Sigviewer, Brian, PyNN, \ldots\\
-\textit{Machine Learning:} PyMVPA, scikits.learn, \ldots\\
-\textit{Imaging:} AFNI, CV, FSL, Lipsia, Mricron, NiPy, \ldots\\
+\textit{Distributed computing:} Condor \\
+\textit{Electrophysiology:} BioSig, EEGLAB, Sigviewer, \ldots\\
+\textit{Machine Learning:} MDP, PyMVPA, sklearn, \ldots\\
+\textit{Neural Modeling:} Brian, PyNN, \ldots\\
+\textit{Imaging:} AFNI, FSL, Mricron, NiPy, SPM, \ldots\\
\textit{Psychophysics:} PsychoPy, Psychtoolbox, \ldots\\
-\vspace{-0.5em}
+\vspace{-0.8em}
+
+% TODO: Environments... -- list avail cloud env using NeuroDebian
\ndsubsection{Benefits from Debian integration}
\item Debian standards and policies guarantee quality and robustness.
\item Debian's centralized bug tracking system provides a unified
- single-point of entry for bug reporting and troubleshooting for any
- software in Debian.
+ single-point of entry for bug reporting and troubleshooting
+ for any software in Debian.
\item Debian makes software available through a world-wide distribution
network, thus offloading bandwidth demands.
software for more than 60 languages.
\end{description}
-\item Neuroscience software becomes a 1st-class citizen within the Debian
- project, which guarantees its availability, longevity, smooth
- installation and upgrades.
+\item Neuroscience software becomes a 1st-class citizen within the
+ Debian project, which guarantees its longevity, smooth installation
+ and upgrades.
%\item Participation in the Debian community helps to assure Debian's
% aptness for the neuroscientific software demands
\ndsubsection{Work-in-progress}
\begin{description}[nolistsep,leftmargin=1pc,style=nextline]
\item[Increased coverage]
-\textit{Electrophysiology:} NEURON, Fieldtrip, \ldots \\
-\textit{Matlab/Octave toolboxes:} SPM, EEGLAB, \ldots \\
-\textit{Distributed computing:} Condor \\
-\textit{Imaging:} CMTK, Freesurfer, \ldots \\
-
-\epigraph{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.}{Prof. Bruce Fischl}{Director, Computational Core at Martinos Center at Massachusetts General Hospital, Charlestown, Massachusetts, USA}
+\textit{Electrophysiology:} Fieldtrip, \ldots \\
+\textit{Neural Modeling:} NEURON, (NEST) \\
+\textit{Imaging:} DTI-TK, Freesurfer, XNAT, \ldots
+% \epigraph{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.}{Prof. Bruce Fischl}{Director, Computational Core at Martinos Center at Massachusetts General Hospital, Charlestown, Massachusetts, USA}
\item[Improved quality assurance]
Extended integration and regression testing
\item[Available snapshotting service]
All versions of packages readily available
\item[Data as the 1st-class citizen]
\url{http://neuro.debian.net/datasets.html}
-\item[Universal availability]
- % \begin{itemize}[nolistsep,leftmargin=1pc,topsep=0em]
- % \item Virtual Appliance enhancements
- %\item
- Cloud computing
- %\end{itemize}
-
+% yoh: see TODO above -- we can say that it is available already
+%\item[Universal availability]
+% % \begin{itemize}[nolistsep,leftmargin=1pc,topsep=0em]
+% % \item Virtual Appliance enhancements
+% %\item
+% Cloud computing
+% %\end{itemize}
\end{description}
\vspace{-0.5em}
\end{flushright}
-
+% TODO yoh: This one remains the best summary IMHO. But may be
+% we would just kick this section out an place Testimonials into References
\epigraph{The approach taken with NeuroDebian is plainly the most appropriate
approach to software distribution for the dominant platform in brain
image analysis, and I have great confidence that this project will be
\ndsubsection{Acknowledgements}
NeuroDebian is grateful to all Debian developers and contributors for
-developing the Debian operating system, and to Prof. James V. Haxby (PBS Department,
-Dartmouth College) for his continued support and endless supply of
-Italian espresso (\url{http://neuro.debian.net/coffeeart.html}).
+developing the Debian operating system, to
+\href{http://www.incf.org}{INCF} for the support in community outreach
+and technical collaborations, and to
+Prof. \href{http://haxbylab.dartmouth.edu}{James V. Haxby}
+(\href{http://www.dartmouth.edu/~psych}{PBS Department, Dartmouth
+ College}) for his continued support and endless supply of Italian
+espresso (\url{http://neuro.debian.net/coffeeart.html}).
+
+
+\ndsubsection{References}
+
+Halchenko, Y. O. \& Hanke, M. (2012). \href{http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full}{Open is not enough. Let’s take the next step: An integrated, community-driven computing platform for neuroscience}. Frontiers in Neuroinformatics, 6:22.
+
+% TODO: adjust for the new layout
+\url{http://neuro.debian.net/#publications}
%\columnbreak
\end{multicols}
+neurodebian (0.29) unstable; urgency=low
+
+ [ Yaroslav Halchenko & Michael Hanke ]
+ * website:
+ - new mirror ([de-md])
+ - dynamic ranges for the new distributions subscription stats plot
+ * VM (6.0.6):
+ - base on 6.0.6 Debian point release (finally version of NeuroDebian
+ VM is in sync with the Debian release)
+ - nd-vmsetupwizard:
+ - robustify check/linking of $HOME/host
+ - optional installations dialog:
+ - set height of the dialog to 450 for to fit all list items
+ - refactored "GIMP" section into "Graphics" which would install
+ also inkscape, vym and svgtune
+ - added sections for "PyMVPA tutorial", and different collections of
+ Python modules (Neuroimaging, Electrophysiology, etc)
+ - Python selections depend on ipython01x instead of older ipython
+ to provide IPython notebooks facilities out-of-the-box
+
+ -- Yaroslav Halchenko <debian@onerussian.com> Mon, 01 Oct 2012 12:26:37 -0400
+
neurodebian (0.28) unstable; urgency=low
[ Michael Hanke & Yaroslav Halchenko]
fi
# create symlink to shared folder into homedir
-[ ! -e $HOME/host ] && ln -s /media/sf_host $HOME/host
+# note: -e check would exit 1 if link is broken
+# ln -f is used for further robustness
+[ ! -L $HOME/host ] && ln -sf /media/sf_host $HOME/host
# TODO: add PyMVPA:
# FALSE "PyMVPA" "python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorial-data" \
# needs -doc and -tutorial-data package
-packages=$(zenity --list $icon_opt --checklist --column="Install" --column="Description" \
+packages=$(zenity --height 450 --list $icon_opt --checklist --column="Install" --column="Description" \
--column="Package Name" --print-column=3 --hide-column=3 --hide-header \
--separator=' ' --text="Please select any additional component that shall be installed.
on the system. No installed packages will be reinstalled or removed, only
additional components will be installed." \
FALSE "Emacs" "emacs" \
-FALSE "GNU Image Manipulation Program (Gimp)" "gimp" \
+FALSE "Graphics (e.g. GIMP, Inscape)" "gimp,inkscape,svgtune,xzgv,vym" \
FALSE "Octave" "octave,qtoctave" \
FALSE "OpenOffice.org" "openoffice.org" \
-FALSE "Scientific Python" "ipython,python-scipy,python-matplotlib" \
+FALSE "PyMVPA Tutorial" "ipython01x,python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorialdata,spyder" \
+FALSE "Python: Electrophysiology & Modeling" "python-brian,python-pynn,python-pyentropy,stimfit" \
+FALSE "Python: Neuroimaging" "ipython01x,spyder,nipy-suite,python-mvpa2" \
+FALSE "Python: Scientific stack" "ipython01x,spyder,python-matplotlib,python-pandas,python-sympy" \
+FALSE "R" "r-recommended" \
FALSE "TeX Live" "texlive" \
FALSE "Adobe Flash browser plugin" "flashplugin-nonfree" \
FALSE "Sun Java browser plugin" "sun-java6-plugin" \
from matplotlib.dates import YearLocator, MonthLocator, DateFormatter
from matplotlib.font_manager import FontProperties
from ConfigParser import SafeConfigParser
-
+from math import ceil
dt = [('ip', '|S16'),
('loc', '|S3'),
('date', float)]
-def make_figure(data, ymax):
+def make_figure(data, ymax=None):
fig = pl.figure(figsize=(14,3))
distros = ('Debian', 'Ubuntu')
# Sorting is actually seems to be not needed on Python 2.7
continue
width = bin_edges[1] - bin_edges[0]
# think lines
- ax.plot(bin_edges[:-1]+(width/2), hist / width,
+ y = hist / width
+ global_y_max = max(max(y), global_y_max)
+ ax.plot(bin_edges[:-1]+(width/2), y,
label=suite, color=colors[i%4], linestyle=linestyle[i//4], lw=2)
# transparent curve shading
ax.fill_between(bin_edges[:-1]+(width/2), 0, hist / width, alpha=0.2,
# figure out axis limits to avoid whitespace in plots
x_max = bin_edges[-2] + width/2
x_min = bin_edges[0] + width/2
- if global_x_max is None or x_max > global_x_max:
- global_x_max = x_max
+
+ global_x_max = max(x_max, global_x_max)
if global_x_min is None or x_min < global_x_min:
global_x_min = x_min
ax.set_ylabel('New subscriptions [1/day]')
if title:
ax.set_title(title)
- if ymax:
- ax.set_ylim(0, ymax)
+ if not ymax:
+ # Always leave significant 5% for improvement ;-)
+ ymax = global_y_max * 1.05
+ ax.set_ylim(0, ymax)
# set x-ticks in date
# see: http://matplotlib.sourceforge.net/examples/api/date_demo.html
ax.xaxis.set_major_locator(YearLocator())
ax.xaxis.set_major_formatter(DateFormatter('\n\n%Y'))
- ax.xaxis.set_minor_locator(MonthLocator())
+ ax.xaxis.set_minor_locator(MonthLocator(interval=2))
ax.xaxis.set_minor_formatter(DateFormatter('%b'))
# format the coords message box
ax.format_xdata = DateFormatter('%Y-%m-%d')
date = datetime.strptime(date, "%d %b %Y")
data.append((ip.strip(), loc, suite, date2num(date)))
data = np.array(data, dtype=dt)
- make_figure(data, ymax=21).savefig(sys.argv[1], bbox_inches='tight', dpi=60)
+ make_figure(data).savefig(sys.argv[1], bbox_inches='tight', dpi=60)
# TODO: arguments later on to become cmdline args
#iso=debian-squeeze-di-beta1-amd64-businesscard.iso
-iso=debian-6.0.3-${ARCH:=amd64}-businesscard.iso
+iso=debian-6.0.6-${ARCH:=amd64}-businesscard.iso
di_cd=$(readlink -f $PWD/../../../neurodebian-images/$iso)
di_host=head1.hydra.dartmouth.edu # where to look for di preseed
build_dir=$PWD/build
dist_dir=$PWD/dist
vendor="NeuroDebian"
-vm_version="6.0.5"
+vm_version="6.0.6"
vm_ostype=Debian
vendor_url="http://neuro.debian.net"
product_url="${vendor_url}/vm.html"
projects / neurodebian.git / commitdiff