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67 \section*{The Universal Operating System}
70 \includegraphics[width=0.5\columnwidth]{openlogo}
71 %\includegraphics[width=0.5\columnwidth]{openlogo-vsop}
73 \url{http://www.debian.org}
74 %\ndsection{Debian GNU/Linux}
82 was founded by Ian Murdock in August 1993 with the goal
83 to create an easy to install and maintain non-commercial GNU/Linux
84 operating system that would be able to compete in the
85 commercial market. Since then, Debian established itself as an
86 independent and unique project driven by more than 3000
87 enthusiastic contributors all around the globe.
88 Principles of \mbox{\emph{do-ocracy}} and democracy backed up by evolving transparent
89 standards allowed Debian to deliver the most comprehensive operating system -- not
90 only by amount of integrated software, but also by
91 number of the supported hardware architectures.
92 % Current installer of Debian has been translated more that to 60 languages.
93 % (12 ??? officially supported architectures).
95 The high quality and openness of Debian made it the foundation of choice for
96 more than 120 derivative GNU/Linux distributions, such as Ubuntu and
99 \ndsubsection{Debian is}
100 \begin{description}[nolistsep,leftmargin=0.8em]
101 \item[V\textnormal{ersatile}]\hfill\url{http://packages.debian.org}\\
102 Over 15000 software packages maintained by experts to provide
103 a stable system for \textit{any} field of application.
104 \item[S\textnormal{ecure}]\hfill\url{http://www.debian.org/security}\\
105 Security updates guarantee safe operation.
107 % \item[S\textnormal{imple}]\blank\\
108 % Single command is enough to install or upgrade single
109 % software or the entire system at once
110 \item[O\textnormal{pen}]\hfill\url{http://www.debian.org/social_contract}\\
111 All software is free and open-source (FOSS).\\
112 Debian is governed by public democratic processes.
113 \item[P\textnormal{opular}]\hfill\url{http://www.debian.org/users}\\
114 Used by governments, companies, educational institutions.
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124 <PROPERTY name="font" value="\usepackage{helvet}"/>
125 <PROPERTY name="fontsize" value="10pt"/>\ndsubsection{Three Debian suites}
127 % Debian distribution comes in 3 major flavors
129 \begin{description}[nolistsep,leftmargin=1pc,topsep=0em]
131 %\item[Unstable] \emph{Constantly changing distribution}\\
132 \item[Development]\hfill\emph{Unstable} (always \emph{sid})\\
133 Never \emph{released}, constantly evolving platform to integrate new
134 versions of software into Debian.\\
135 %entry point for the software to appear in Debian.\\
136 Despite its name, \emph{Unstable} is a good platform for those
137 requiring the most recent versions of software.
139 %\item[Testing] \emph{Constantly changing future release candidate}\\
140 \item[``Always-ready-to-release'']\hfill\emph{Testing} (now \emph{jessie})\\
141 % What to become a next \emph{Stable} release candidate.\\
142 Software versions known to be secure and of good quality.
143 % Software migrated from \emph{Unstable} which is known to be of good
144 % quality. Immediate updates are provided only
145 % to assure secure and robust performance. \\
146 \emph{Testing} provides a good balance between stability and recency
149 %\item[Stable] \emph{Official release}\\
150 \item[Official release]\hfill\emph{Stable} (now 7.5, \emph{wheezy})\\
151 % Software verified to be well tested and secure,
152 % Very stable (hence the name) and secure
153 % but might be lacking the most recent versions.\\% of the software.\\
154 % of not the most recent versions. \\
155 \emph{Stable} is released ``when it is ready'', \emph{i.e.} when
156 \emph{Testing} is assured to be robust. %, on average bi-yearly.
157 Complementary updates keep the
159 \emph{Stable} is the best choice where reliability and security are of
163 \ndsubsection{Three Debian components}
165 % Debian distribution comes in 3 major flavors
166 %Debian Free Software Guidelines (DFSG)\\
167 %\url{http://www.debian.org/social_contract}
169 \begin{description}[nolistsep,leftmargin=1pc,topsep=0em]
170 \item[Free as in freedom]\hfill\emph{main}\\
171 % This is the actual Debian with full support.\\
172 All software in \emph{main} is distributed under FOSS licenses
173 compliant with Debian Free Software Guidelines (DFSG) to assure
174 complete freedom to use, modify, and (re-)distribute.
175 \item[Wanna-be free]\hfill\emph{contrib}\\
176 FOSS depending on \emph{non-free} 3rd party software.
177 % Software which, despite being free itself, depends on
178 % \emph{non-free} 3rd party software, rendering it useless without
179 \item[Somewhat free]\hfill\emph{non-free}\\
180 Software under restrictive licenses available at no charge.
181 % removing some freedoms
182 % (\emph{e.g.} non-commercial use only), but which is allowed to be
183 % used for free and re-distributed (\emph{e.g. NVidia drivers})
187 \ndsubsection{Who is Debian}
188 % could be simply 'Debian People' or 'Debian Community'
190 Debian is the only major operating system developed
191 solely by volunteer individuals who collaborate via the Internet.
192 Debian developers, teams or individual contributors improve the operating
193 system not by writing new applications (in most cases) but by
194 \begin{itemize}[nolistsep,topsep=0em,leftmargin=1pc]
195 \item integrating existing software into Debian
196 \item fixing and communicating bug reports to original developers
197 \item assuring overall quality of the distribution
198 \item improving documentation and translations
199 \item providing user support
202 Packaged software in Debian have individual maintainers who are
203 often also users of a particular software, and who are therefore interested in its
204 reliable operation. Certain fields of applications have dedicated maintainer
205 teams, such as Debian-Science or Debian-Med.
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212 <LATEX ConfigFile="100_latex.xml" DPI="0" USE_PREAMBLE="1">
213 <PROPERTY name="additionalheaders" value="\usepackage{color} \usepackage{flowfram} \usepackage{tabularx} % for column-width tables \usepackage[table]{xcolor} % color control \usepackage[colorlinks]{hyperref} \usepackage{graphicx} \graphicspath{ {/home/mih/hacking/neurodebian/artwork/} } \usepackage{enumitem} % useful for control of listings \usepackage[compact,raggedright]{titlesec} \newcommand{\epigraph}[3]{\textit{#1}\linebreak \vspace{-1.5em} \begin{flushright}\hspace{5em}\ --\ #2\linebreak\small{#3} \end{flushright}} \pagestyle{empty} \parindent=0pt % To create tables within multicols \makeatletter \newenvironment{ndtable} {\def\@captype{table}} {} \newcommand{\ndheading}[3]{% \vspace{0.5em} \begin{ndtable}% \rowcolors[\hline]{1}{#2}{} \arrayrulecolor{#3} \begin{tabularx}{\columnwidth}{>{\centering\arraybackslash}X}\vspace{-.5em}\normalfont\large\bfseries #1\vspace{0.05em}\\\end{tabularx} \end{ndtable} \vspace{-.5em} } \definecolor{secfgcol}{RGB}{215, 6, 83} \definecolor{secbgcol}{RGB}{255, 241, 248} \newcommand{\ndsection}[1]{\ndheading{#1}{secbgcol}{secfgcol}} \newcommand{\ndsubsection}[1]{\ndheading{#1}{secbgcol}{secfgcol}} "/>
214 <PROPERTY name="font" value="\usepackage{helvet}"/>
215 <PROPERTY name="fontsize" value="10pt"/>\ndsubsection{How to get Debian}
217 %\subsubsection*{Stable}
218 \begin{description}[nolistsep,leftmargin=1pc,style=nextline]
219 \item[Install on a hard-drive] \url{http://www.debian.org/distrib/}
220 \item[Live CD/DVD] \url{http://www.debian.org/CD/live/}
221 \item[Run in a Virtual Machine] \url{http://neuro.debian.net/vm.html}
222 \item[Development version] \url{http://www.debian.org/devel/debian-installer}
223 \item[Use in a cloud] \url{https://wiki.debian.org/Cloud}
226 % \ndsubsection{Get \emph{Testing/Unstable} Debian}
228 % Install on a hard-drive or in a Virtual Machine\\
229 % \url{http://www.debian.org/devel/debian-installer}
232 \ndsubsection{How to install software}
234 GUI (Synaptic): \textit{Select and click ``Apply''}\\
237 \includegraphics[width=0.95\columnwidth]{shots/synaptic-fslview}
241 Command line: \texttt{apt-get install <packagename>}
245 \ndsubsection{How to upgrade the entire system}
249 \quad\textit{Click ``Mark All Upgrades'', ``Apply''}\\
252 \quad\texttt{apt-get update; apt-get dist-upgrade}
254 \ndsubsection{How to get support}
256 \hspace{1em}\url{http://www.debian.org/support}
258 \begin{description}[nolistsep,leftmargin=1pc,style=nextline]
262 % Use \emph{Synaptic Package Manager}
264 \texttt{reportbug <packagename>}
266 \url{http://www.debian.org/MailingLists}\\
267 \url{http://forums.debian.net}, \url{http://ask.debian.net}\\
268 \url{http://www.debian.org/consultants}
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276 <LATEX ConfigFile="100_latex.xml" DPI="0" USE_PREAMBLE="1">
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278 <PROPERTY name="font" value="\usepackage{helvet}"/>
279 <PROPERTY name="fontsize" value="10pt"/>\section*{The Universal Research Platform}
281 \includegraphics[width=\columnwidth]{logo_tuned/label}
282 \url{http://neuro.debian.net}
283 %\ndsection{NeuroDebian Project:}
287 \ndsection{NeuroDebian is}
289 a Debian project that provides the Neuroscience community with a
290 stable and versatile research platform -- the Debian operating system.
291 Since 2005, \mbox{NeuroDebian} integrates neuroscience software into Debian
292 to allow neuroscientists to benefit from the advantages of
293 the universal operating system in their day-to-day research activities.
294 The NeuroDebian repository
295 (\url{http://neuro.debian.net}) offers the latest research software for
296 all Debian suites (and various releases of Ubuntu).
297 The combination of a stable generic
298 operating system, Debian, and a variety of conveniently accessible research
299 software creates a versatile research platform for neuroscience that offers the
300 latest methodologies of the field to everyone, for free.
301 These advantages make NeuroDebian increasingly popular among
302 neuroscientists and scientific software developers.
306 \ndsubsection{NeuroDebian is NOT}
308 yet another Debian GNU/Linux derivative distribution. All work done
309 by the NeuroDebian project targets the official Debian operating system. This
310 approach helps to increase the longevity of the project by relying on the
311 efforts of thousands of Debian contributors.
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317 <LATEX ConfigFile="100_latex.xml" DPI="0" USE_PREAMBLE="1">
318 <PROPERTY name="additionalheaders" value="\usepackage{color} \usepackage{flowfram} \usepackage{tabularx} % for column-width tables \usepackage[table]{xcolor} % color control \usepackage[colorlinks]{hyperref} \usepackage{graphicx} \graphicspath{ {/home/mih/hacking/neurodebian/artwork/} {/home/mih/hacking/neurodebian/artwork/shots} } \usepackage{enumitem} % useful for control of listings \usepackage[compact,raggedright]{titlesec} \newcommand{\epigraph}[3]{\textit{#1}\linebreak \vspace{-1.5em} \begin{flushright}\hspace{5em}\ --\ #2\linebreak\small{#3} \end{flushright}} \pagestyle{empty} \parindent=0pt % To create tables within multicols \makeatletter \newenvironment{ndtable} {\def\@captype{table}} {} \newcommand{\ndheading}[3]{% \vspace{0.5em} \begin{ndtable}% \rowcolors[\hline]{1}{#2}{} \arrayrulecolor{#3} \begin{tabularx}{\columnwidth}{>{\centering\arraybackslash}X}\vspace{-.5em}\normalfont\large\bfseries #1\vspace{0.05em}\\\end{tabularx} \end{ndtable} \vspace{-.5em} } \definecolor{secfgcol}{RGB}{215, 6, 83} \definecolor{secbgcol}{RGB}{255, 241, 248} \newcommand{\ndsection}[1]{\ndheading{#1}{secbgcol}{secfgcol}} \newcommand{\ndsubsection}[1]{\ndheading{#1}{secbgcol}{secfgcol}} "/>
319 <PROPERTY name="font" value="\usepackage{helvet}"/>
320 <PROPERTY name="fontsize" value="10pt"/>\ndsubsection{Software at your fingertips}
323 \url{http://neuro.debian.net/pkgs.html}
326 \textit{Distributed computing:} Condor, DMTCP, IPython, \ldots \\
327 \textit{Electrophysiology:} BioSig, Neo, Sigviewer, \ldots\\
328 \textit{Machine Learning:} MDP, PyMVPA, sklearn, \ldots\\
329 \textit{Neural Modeling:} Brian, CNrun, PyNN, XPPAUT \ldots\\
330 \textit{Imaging:} AFNI, CMTK, FSL, Mricron, NiPy \ldots\\
331 \textit{Psychophysics:} PsychoPy, Psychtoolbox-3, PyEPL \ldots\\
334 % TODO: Environments... -- list avail cloud env using NeuroDebian
336 \ndsubsection{Benefits from Debian integration}
338 \begin{itemize}[nolistsep,leftmargin=1pc]
340 % rephrase to outline the benefit, not burden
341 \item Debian standards and policies guarantee quality and robustness.
343 \item Debian's centralized bug tracking system provides a unified
344 single-point of entry for bug reporting and troubleshooting
345 for any software in Debian.
347 \item Debian makes software available through a world-wide distribution
348 network, thus offloading bandwidth demands.
350 \item Other Debian contributors handle large-scale aspects of
351 deployment, quality assurance, porting and integration at the level
352 of the entire distribution:
354 \begin{description}[nolistsep,leftmargin=1pc]
355 \item[Porting] Software sources get built for 11 hardware
356 architectures and 3 kernels (Linux, HURD, kFreeBSD). Porter teams
357 maintain build infrastructure and help make the code
359 \item[QA] Whole-archive rebuilds assure robustness of packaging and
360 warn about upcoming problems (core libraries upgrades) beforehand.
361 \item[Internationalization (I18n)] Translator teams help localize
362 software for more than 60 languages.
365 \item Neuroscience software becomes a 1st-class citizen within the
366 Debian project, which guarantees its longevity, smooth installation
369 %\item Participation in the Debian community helps to assure Debian's
370 % aptness for the neuroscientific software demands
374 \ndsubsection{How to get NeuroDebian}
376 \textit{Debian/Ubuntu:} \url{neuro.debian.net} repository \\
377 \textit{Others:} NeuroDebian Virtual Machine
379 % Here place a left-top corner of OSX with seamless mode
381 \includegraphics[width=\columnwidth]{shots/mac_vm_mricron}
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388 <LATEX ConfigFile="100_latex.xml" DPI="0" USE_PREAMBLE="1">
389 <PROPERTY name="additionalheaders" value="\usepackage{color} \usepackage{flowfram} \usepackage{tabularx} % for column-width tables \usepackage[table]{xcolor} % color control \usepackage[colorlinks]{hyperref} \usepackage{graphicx} \graphicspath{ {/home/mih/hacking/neurodebian/artwork/} {/home/mih/hacking/neurodebian/artwork/shots} } \usepackage{enumitem} % useful for control of listings \usepackage[compact,raggedright]{titlesec} \newcommand{\epigraph}[3]{\textit{#1}\linebreak \vspace{-1.5em} \begin{flushright}\hspace{5em}\ --\ #2\linebreak\small{#3} \end{flushright}} \pagestyle{empty} \parindent=0pt % To create tables within multicols \makeatletter \newenvironment{ndtable} {\def\@captype{table}} {} \newcommand{\ndheading}[3]{% \vspace{0.5em} \begin{ndtable}% \rowcolors[\hline]{1}{#2}{} \arrayrulecolor{#3} \begin{tabularx}{\columnwidth}{>{\centering\arraybackslash}X}\vspace{-.5em}\normalfont\large\bfseries #1\vspace{0.05em}\\\end{tabularx} \end{ndtable} \vspace{-.5em} } \definecolor{secfgcol}{RGB}{215, 6, 83} \definecolor{secbgcol}{RGB}{255, 241, 248} \newcommand{\ndsection}[1]{\ndheading{#1}{secbgcol}{secfgcol}} \newcommand{\ndsubsection}[1]{\ndheading{#1}{secbgcol}{secfgcol}} "/>
390 <PROPERTY name="font" value="\usepackage{helvet}"/>
391 <PROPERTY name="fontsize" value="10pt"/>\ndsubsection{Work-in-progress}
392 \begin{description}[nolistsep,leftmargin=1pc,style=nextline]
393 \item[Increased coverage]
394 \textit{Electrophysiology:} Fieldtrip \\
395 \textit{Neural Modeling:} NEURON, (NEST), LFPy \\
396 \textit{Imaging:} DTI-TK, Freesurfer, XNAT, \ldots
397 % \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}
398 \item[Improved quality assurance]
399 Extended integration and regression testing\\
400 \url{http://testkraut.readthedocs.org}
401 \item[Available snapshotting service]
402 % Entire NeuroDebian repository for any given past moment
403 All versions of packages readily available
404 \item[Data as the 1st-class citizen]
405 \url{http://neuro.debian.net/datasets.html}\\
406 \url{http://github.com/neurodebian/datagit}
407 % yoh: see TODO above -- we can say that it is available already
408 %\item[Universal availability]
409 % % \begin{itemize}[nolistsep,leftmargin=1pc,topsep=0em]
410 % % \item Virtual Appliance enhancements
417 \ndsubsection{Testimonials}
420 \url{http://neuro.debian.net/testimonials.html}
423 % TODO yoh: This one remains the best summary IMHO. But may be
424 % we would just kick this section out an place Testimonials into References
425 \epigraph{The approach taken with NeuroDebian is plainly the most appropriate
426 approach to software distribution for the dominant platform in brain
427 image analysis, and I have great confidence that this project will be
428 a major asset to the neuroscience community in facilitating the
429 distribution of stable software, improving the reliability and
430 replicability of analyses, and in helping to improve software
431 :RENDER FRAME: updateImage(): "Running the external application failed!"
432 development practices.}{Prof. Daniel Y. Kimberg}{Director, Data
433 Processing Facility, Center for Functional Neuroimaging, University of
434 Pennsylvania, Philadelphia, USA}
436 \ndsubsection{Acknowledgements}
438 NeuroDebian is grateful to all Debian developers and contributors for
439 developing the Debian operating system, to
440 \href{http://www.incf.org}{INCF} for the support in community outreach
441 and technical collaborations, and to
442 Prof. \href{http://haxbylab.dartmouth.edu}{James V. Haxby}
443 (\href{http://www.dartmouth.edu/~psych}{PBS Department, Dartmouth
444 College}) for his continued support and endless supply of Italian
445 espresso (\url{http://neuro.debian.net/coffeeart.html}).
448 \ndsubsection{References}
450 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.
452 % TODO: adjust for the new layout
453 \url{http://neuro.debian.net/#publications}
455 <PageItemAttributes/>