\ndsection{Debian}
was founded by Ian Murdock in August 1993 with the goal
-to create an easy-to-install and maintain non-commercial GNU/Linux
+to create an easy to install and maintain non-commercial GNU/Linux
operating system that would be able to compete in the
-commercial market. Since then Debian established itself as an
+commercial market. Since then, Debian established itself as an
independent and unique project driven by more than 3000
enthusiastic contributors all around the globe.
-Principles of \emph{do-ocracy} and democracy backed up by evolving transparent
+Principles of \mbox{\emph{do-ocracy}} and democracy backed up by evolving transparent
standards allowed Debian to deliver the most comprehensive operating system -- not
only by amount of integrated software, but also by
number of the supported hardware architectures.
requiring the most recent versions of software.
%\item[Testing] \emph{Constantly changing future release candidate}\\
-\item[``Almost-ready-to-release'']\hfill\emph{Testing} (now \emph{squeeze})\\
+\item[``Always-ready-to-release'']\hfill\emph{Testing} (now \emph{jessie})\\
% What to become a next \emph{Stable} release candidate.\\
Software versions known to be secure and of good quality.
% Software migrated from \emph{Unstable} which is known to be of good
of software.
%\item[Stable] \emph{Official release}\\
-\item[Official release]\hfill\emph{Stable} (now \emph{lenny})\\
+\item[Official release]\hfill\emph{Stable} (now 7.7, \emph{wheezy})\\
% Software verified to be well tested and secure,
% Very stable (hence the name) and secure
% but might be lacking the most recent versions.\\% of the software.\\
\emph{Testing} is assured to be robust. %, on average bi-yearly.
Complementary updates keep the
system secure. \\
- \emph{Stable} is the choice where stability and security are of
+ \emph{Stable} is the best choice where reliability and security are of
primary importance.
\end{description}
\ndsubsection{It has names}
The code names of Debian releases are names of characters from the Toy
-Story animation, e.g. sid, squeeze, lenny. \emph{Unstable}
+Story animation, \emph{e.g.} sid, jessie, wheezy. \emph{Unstable}
flavor always called \emph{sid}, while a new name chosen for every
upcoming release and assigned to \emph{Testing} to become a code name
of the release when it becomes \emph{Stable}.\\ At the moment
-\emph{squeeze} is \emph{Testing}, and \emph{lenny} is \emph{Stable}.
-As soon as \emph{squeeze} gets released, \emph{Testing} will be given
-a new name -- \emph{wheezy}.
+\emph{jessie} is \emph{Testing} (actually \emph{Frozen} in preparation
+for the release), and \emph{wheezy} is \emph{Stable}.
+As soon as \emph{jessie} gets released, \emph{Testing} will be given
+a new name.% -- \emph{jessie}.
\end{comment}
\ndsubsection{Three Debian components}
\end{description}
-\ndsubsection{Debian enthusiastic experts}
+\ndsubsection{Who is Debian}
% could be simply 'Debian People' or 'Debian Community'
Debian is the only major operating system developed
solely by volunteer individuals who collaborate via the Internet.
Debian developers, teams or individual contributors improve the operating
-system not by writing new applications (in most cases), but by
+system not by writing new applications (in most cases) but by
\begin{itemize}[nolistsep,topsep=0em,leftmargin=1pc]
\item integrating existing software into Debian
\item fixing and communicating bug reports to original developers
%\subsubsection*{Stable}
\begin{description}[nolistsep,leftmargin=1pc,style=nextline]
-\item[Install on a hard-drive] \url{http://get.debian.net/}
-\item[Boot from CD/USB] \url{http://get.debian.net/live/}
+\item[Install on a hard-drive] \url{http://www.debian.org/distrib/}
+\item[Live CD/DVD] \url{http://www.debian.org/CD/live/}
\item[Run in a Virtual Machine] \url{http://neuro.debian.net/vm.html}
-\item[More options (e.g. buy pre-installed machine)] \url{http://debian.org/distrib}
-\item[Testing/Unstable version] \url{http://www.debian.org/devel/debian-installer}
+\item[Development version] \url{http://www.debian.org/devel/debian-installer}
+\item[Use in a cloud] \url{https://wiki.debian.org/Cloud}
+\item[Docker: \texttt{docker pull debian}]
\end{description}
% \ndsubsection{Get \emph{Testing/Unstable} Debian}
% Install on a hard-drive or in a Virtual Machine\\
% \url{http://www.debian.org/devel/debian-installer}
%
-
+\vspace{-1em}
\ndsubsection{How to install software}
GUI (Synaptic): \textit{Select and click ``Apply''}\\
-\includegraphics[width=\columnwidth]{shots/synaptic-fslview}
+\begin{center}
+\vspace{-1.2em}
+\includegraphics[width=0.95\columnwidth]{shots/synaptic-fslview}
+\vspace{-0.7em}
+\end{center}
Command line: \texttt{apt-get install <packagename>}
\ndsubsection{How to get support}
-\url{http://www.debian.org/support}
+\hspace{1em}\url{http://www.debian.org/support}
\begin{description}[nolistsep,leftmargin=1pc,style=nextline]
+%\item[Overview]
+
%\item[GUI]
% Use \emph{Synaptic Package Manager}
\item[Software bug]
%\item[Mailing lists]
\url{http://www.debian.org/MailingLists}\\
\url{http://forums.debian.net}\\
- \url{http://ask.debian.net}
+ \url{http://ask.debian.net}\\
+ \url{irc://irc.debian.org/debian}
%\end{description}
\item[Commercial support]
\url{http://www.debian.org/consultants}
\ndsection{NeuroDebian is}
a Debian project that provides the Neuroscience community with a
-stable and versatile research platform -- the Debian OS.
-Since 2005, NeuroDebian integrates neuroscience software into the Debian
-operating system to allow neuroscientists to benefit from the advantages of
+stable and versatile research platform -- the Debian operating system.
+Since 2005, \mbox{NeuroDebian} integrates neuroscience software into Debian
+to allow neuroscientists to benefit from the advantages of
the universal operating system in their day-to-day research activities.
The NeuroDebian repository
(\url{http://neuro.debian.net}) offers the latest research software for
\vspace{3em}
\columnbreak
-\ndsubsection{NeuroDebian software coverage}
+\ndsubsection{Software at your fingertips}
\begin{flushright}
\vspace{-0.5em}
\url{http://neuro.debian.net/pkgs.html}
+\vspace{-0.1em}
\end{flushright}
-\textit{Electrophysiology:} BioSig, Sigviewer, Brian, \ldots\\
-\textit{Machine Learning:} PyMVPA, scikits.learn, \ldots\\
-\textit{Imaging:} AFNI, FSL, Mricron, NiPy, Voxbo, \ldots\\
-\textit{Psychophysics:} PsychoPy, PyEPL, PyOptical, \ldots\\
-\vspace{-0.5em}
+\textit{Distributed computing:} Condor, DMTCP, IPython, \ldots \\
+\textit{Electrophysiology:} BioSig, Neo, Sigviewer, \ldots\\
+\textit{Machine Learning:} MDP, PyMVPA, sklearn, \ldots\\
+\textit{Neural Modeling:} Brian, CNrun, PyNN, XPPAUT \ldots\\
+\textit{Imaging:} AFNI, CMTK, FSL, Mricron, NiPy \ldots\\
+\textit{Psychophysics:} PsychoPy, Psychtoolbox-3, PyEPL \ldots\\
+\vspace{-0.8em}
+
+% TODO: Environments... -- list avail cloud env using NeuroDebian
\ndsubsection{Benefits from Debian integration}
\begin{itemize}[nolistsep,leftmargin=1pc]
% rephrase to outline the benefit, not burden
-\item Debian standards and policies guarantee quality and robustness
+\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
+ network, thus offloading bandwidth demands.
\item Other Debian contributors handle large-scale aspects of
deployment, quality assurance, porting and integration at the level
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, OpenElectrophy, \ldots \\
-\textit{Matlab/Octave toolboxes:} SPM, EEGLAB, \ldots \\
-\textit{Distributed computing:} Condor \\
-\textit{Imaging:} Connectomeviewer, Freesurfer, MIPAV \\
-
-\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 \\
+\textit{Neural Modeling:} NEURON, (NEST), LFPy \\
+\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
+ Extended integration and regression testing\\
+ \url{http://testkraut.readthedocs.org}
\item[Available snapshotting service]
% Entire NeuroDebian repository for any given past moment
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}
-
+\item[Data as the 1st-class citizen]
+ \url{http://datalad.org} data distribution
+\item[Community knowledge exchange portal]
+ \url{http://community.neurodebian.org}
+% 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 the
-development of Debian OS, 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}).
+NeuroDebian is grateful to all Debian developers and contributors for
+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}
projects / neurodebian.git / blobdiff