1 %-*- mode: latex; fill-column: 70 -*-
2 % ex: set sts=4 ts=4 sw=4 et tw=70:
5 \documentclass[letterpaper,landscape]{report}
6 \usepackage[landscape,margin=0.5cm]{geometry}
9 %\usepackage{booktabs} % for rules in tables
10 \usepackage{tabularx} % for column-width tables
11 \usepackage[table]{xcolor} % color control
13 \usepackage[colorlinks]{hyperref}
16 %\setlength{\columnseprule}{1pt} % for visible divider
17 \setlength{\columnsep}{1cm}
24 \usepackage{enumitem} % useful for control of listings
25 \usepackage[compact,raggedright]{titlesec}
28 \newcommand{\epigraph}[3]{\textit{#1}\linebreak \vspace{-1.5em} \begin{flushright}\hspace{5em}\ --\ #2\linebreak\small{#3} \end{flushright}}
33 % Attempts to change bg color of *section headings
34 %\definecolor{secbgcol}{rgb}{0.9, 0.85, 0.85}
35 %\titleformat{\section}
36 %{\color{red}\normalfont\Large\bfseries}{\ndsection}{1em}{}
37 %\titleformat{\subsection}
38 %{\color{red}\normalfont\large\bfseries}{\begin{flushright}\hfill\thesubsection
39 % \end{flushright}}{1em}{}
41 %\usepackage{pstricks}
43 % To create tables within multicols
45 \newenvironment{ndtable}
46 {\def\@captype{table}}
50 \newcommand{\ndheading}[3]{%
53 \rowcolors[\hline]{1}{#2}{} \arrayrulecolor{#3}
54 \begin{tabularx}{\columnwidth}{>{\centering\arraybackslash}X}\vspace{-.5em}\normalfont\large\bfseries
55 #1\vspace{0.05em}\\\end{tabularx}
60 \definecolor{secfgcol}{RGB}{215, 6, 83}
61 \definecolor{secbgcol}{RGB}{255, 241, 248}
62 \newcommand{\ndsection}[1]{\ndheading{#1}{secbgcol}{secfgcol}}
63 \newcommand{\ndsubsection}[1]{\ndheading{#1}{secbgcol}{secfgcol}}
71 \begin{multicols}{3} % 3 columns
73 \section*{The Universal Operating System}
76 \includegraphics[width=0.5\columnwidth]{openlogo}
77 %\includegraphics[width=0.5\columnwidth]{openlogo-vsop}
79 \url{http://www.debian.org}
80 %\ndsection{Debian GNU/Linux}
88 was founded by Ian Murdock in August 1993 with the goal
89 to create an easy to install and maintain non-commercial GNU/Linux
90 operating system that would be able to compete in the
91 commercial market. Since then, Debian established itself as an
92 independent and unique project driven by more than 3000
93 enthusiastic contributors all around the globe.
94 Principles of \mbox{\emph{do-ocracy}} and democracy backed up by evolving transparent
95 standards allowed Debian to deliver the most comprehensive operating system -- not
96 only by amount of integrated software, but also by
97 number of the supported hardware architectures.
98 % Current installer of Debian has been translated more that to 60 languages.
99 % (12 ??? officially supported architectures).
101 The high quality and openness of Debian made it the foundation of choice for
102 more than 120 derivative GNU/Linux distributions, such as Ubuntu and
105 \ndsubsection{Debian is}
106 \begin{description}[nolistsep,leftmargin=0.8em]
107 \item[V\textnormal{ersatile}]\hfill\url{http://packages.debian.org}\\
108 Over 15000 software packages maintained by experts to provide
109 a stable system for \textit{any} field of application.
110 \item[S\textnormal{ecure}]\hfill\url{http://www.debian.org/security}\\
111 Security updates guarantee safe operation.
113 % \item[S\textnormal{imple}]\blank\\
114 % Single command is enough to install or upgrade single
115 % software or the entire system at once
116 \item[O\textnormal{pen}]\hfill\url{http://www.debian.org/social_contract}\\
117 All software is free and open-source (FOSS).\\
118 Debian is governed by public democratic processes.
119 \item[P\textnormal{opular}]\hfill\url{http://www.debian.org/users}\\
120 Used by governments, companies, educational institutions.
124 Original: Very Special Old Pale
127 Very (Special|Stable) Operating Platform
130 %\ndsection{Understand Debian}
132 \ndsubsection{Three Debian suites}
134 % Debian distribution comes in 3 major flavors
136 \begin{description}[nolistsep,leftmargin=1pc,topsep=0em]
138 %\item[Unstable] \emph{Constantly changing distribution}\\
139 \item[Development]\hfill\emph{Unstable} (always \emph{sid})\\
140 Never \emph{released}, constantly evolving platform to integrate new
141 versions of software into Debian.\\
142 %entry point for the software to appear in Debian.\\
143 Despite its name, \emph{Unstable} is a good platform for those
144 requiring the most recent versions of software.
146 %\item[Testing] \emph{Constantly changing future release candidate}\\
147 \item[``Always-ready-to-release'']\hfill\emph{Testing} (now \emph{jessie})\\
148 % What to become a next \emph{Stable} release candidate.\\
149 Software versions known to be secure and of good quality.
150 % Software migrated from \emph{Unstable} which is known to be of good
151 % quality. Immediate updates are provided only
152 % to assure secure and robust performance. \\
153 \emph{Testing} provides a good balance between stability and recency
156 %\item[Stable] \emph{Official release}\\
157 \item[Official release]\hfill\emph{Stable} (now 7.2, \emph{wheezy})\\
158 % Software verified to be well tested and secure,
159 % Very stable (hence the name) and secure
160 % but might be lacking the most recent versions.\\% of the software.\\
161 % of not the most recent versions. \\
162 \emph{Stable} is released ``when it is ready'', \emph{i.e.} when
163 \emph{Testing} is assured to be robust. %, on average bi-yearly.
164 Complementary updates keep the
166 \emph{Stable} is the best choice where reliability and security are of
171 \ndsubsection{It has names}
173 The code names of Debian releases are names of characters from the Toy
174 Story animation, \emph{e.g.} sid, jessie, wheezy. \emph{Unstable}
175 flavor always called \emph{sid}, while a new name chosen for every
176 upcoming release and assigned to \emph{Testing} to become a code name
177 of the release when it becomes \emph{Stable}.\\ At the moment
178 \emph{jessie} is \emph{Testing}, and \emph{wheezy} is \emph{Stable}.
179 As soon as \emph{jessie} gets released, \emph{Testing} will be given
180 a new name.% -- \emph{jessie}.
183 \ndsubsection{Three Debian components}
185 % Debian distribution comes in 3 major flavors
186 %Debian Free Software Guidelines (DFSG)\\
187 %\url{http://www.debian.org/social_contract}
189 \begin{description}[nolistsep,leftmargin=1pc,topsep=0em]
190 \item[Free as in freedom]\hfill\emph{main}\\
191 % This is the actual Debian with full support.\\
192 All software in \emph{main} is distributed under FOSS licenses
193 compliant with Debian Free Software Guidelines (DFSG) to assure
194 complete freedom to use, modify, and (re-)distribute.
195 \item[Wanna-be free]\hfill\emph{contrib}\\
196 FOSS depending on \emph{non-free} 3rd party software.
197 % Software which, despite being free itself, depends on
198 % \emph{non-free} 3rd party software, rendering it useless without
199 \item[Somewhat free]\hfill\emph{non-free}\\
200 Software under restrictive licenses available at no charge.
201 % removing some freedoms
202 % (\emph{e.g.} non-commercial use only), but which is allowed to be
203 % used for free and re-distributed (\emph{e.g. NVidia drivers})
207 \ndsubsection{Who is Debian}
208 % could be simply 'Debian People' or 'Debian Community'
210 Debian is the only major operating system developed
211 solely by volunteer individuals who collaborate via the Internet.
212 Debian developers, teams or individual contributors improve the operating
213 system not by writing new applications (in most cases) but by
214 \begin{itemize}[nolistsep,topsep=0em,leftmargin=1pc]
215 \item integrating existing software into Debian
216 \item fixing and communicating bug reports to original developers
217 \item assuring overall quality of the distribution
218 \item improving documentation and translations
219 \item providing user support
222 Packaged software in Debian have individual maintainers who are
223 often also users of a particular software, and who are therefore interested in its
224 reliable operation. Certain fields of applications have dedicated maintainer
225 teams, such as Debian-Science or Debian-Med.
228 \ndsubsection{How to get Debian}
230 %\subsubsection*{Stable}
231 \begin{description}[nolistsep,leftmargin=1pc,style=nextline]
232 \item[Install on a hard-drive] \url{http://www.debian.org/distrib/}
233 \item[Live CD/DVD] \url{http://www.debian.org/CD/live/}
234 \item[Run in a Virtual Machine] \url{http://neuro.debian.net/vm.html}
235 \item[Development version] \url{http://www.debian.org/devel/debian-installer}
236 \item[Use in a cloud] \url{https://wiki.debian.org/Cloud}
239 % \ndsubsection{Get \emph{Testing/Unstable} Debian}
241 % Install on a hard-drive or in a Virtual Machine\\
242 % \url{http://www.debian.org/devel/debian-installer}
245 \ndsubsection{How to install software}
247 GUI (Synaptic): \textit{Select and click ``Apply''}\\
250 \includegraphics[width=0.95\columnwidth]{shots/synaptic-fslview}
254 Command line: \texttt{apt-get install <packagename>}
258 \ndsubsection{How to upgrade the entire system}
262 \quad\textit{Click ``Mark All Upgrades'', ``Apply''}\\
265 \quad\texttt{apt-get update; apt-get dist-upgrade}
267 \ndsubsection{How to get support}
269 \hspace{1em}\url{http://www.debian.org/support}
271 \begin{description}[nolistsep,leftmargin=1pc,style=nextline]
275 % Use \emph{Synaptic Package Manager}
277 \texttt{reportbug <packagename>}
278 \item[Community support]
279 %\begin{description}[nolistsep,leftmargin=1pc]
280 %\item[Mailing lists]
281 \url{http://www.debian.org/MailingLists}\\
282 \url{http://forums.debian.net}\\
283 \url{http://ask.debian.net}\\
284 \url{irc://irc.debian.org/debian}
286 \item[Commercial support]
287 \url{http://www.debian.org/consultants}
291 \ndsection{Reasons to choose Debian}
292 \paragraph{It is maintained by its users}
294 If something needs to be fixed or improved, we just do it.
296 \paragraph{Unparalleled support}
298 Mail sent to the mailing lists often gets answers within 15 minutes (or less),
299 for free, and by the people who developed it. Compare that to typical phone
300 support: hours spent on the phone, for money, only to get someone who doesn't
301 know the system well enough to even understand your question.
303 \paragraph{You wouldn't be alone in your choice}
305 A wide range of organizations and individuals use Debian. See our Who's Using
306 Debian? page for a description of some high-profile sites which use Debian, and
307 have chosen to submit a short description of how they use Debian and why.
309 \paragraph{The best packaging system in the world.}
311 Tired of old files from software three versions old cluttering your system? Or
312 installing a piece of software only to find it causes your system to crash
313 because of software conflicts? Dpkg, Debian's endured packaging system, takes
314 care of these issues for you.
316 \paragraph{Easy installation}
318 If you have heard that GNU/Linux is difficult to install, then you haven't
319 tried Debian lately. We are constantly improving the installation process. You
320 can do the installation directly from CD, DOS, floppies or even over the
323 \paragraph{Incredible amounts of software}
325 Debian comes with over 25000 different pieces of software. Every bit of it is
326 free. If you have proprietary software that runs under GNU/Linux, you can still
327 use it - in fact, there may even be an installer in Debian that will
328 automatically install and set up everything for you.
330 \paragraph{Packages well integrated}
332 Debian surpasses all other distributions in how well its packages are
333 integrated. Since all software is packaged by a coherent group, not only can
334 all packages be found at a single site, but you can be assured that we have
335 already worked out all issues regarding complicated dependencies. While we feel
336 that the deb format has some advantages over the rpm format, it is the
337 integration between the packages that makes a Debian system more robust.
339 \paragraph{Source code}
341 If you are a software developer, you will appreciate the fact that there are
342 hundreds of development tools and languages, plus millions of lines of source
343 code in the base system. All of the software in the main distribution meets the
344 criteria of the Debian Free Software Guidelines (DFSG). This means that you can
345 freely use this code to study from, or to incorporate into new free software
346 projects. There are also plenty of tools and code suitable for use in
347 proprietary projects.
349 \paragraph{Easy upgrades}
351 Due to our packaging system, upgrading to a new version of Debian is a snap.
352 Just run apt-get update ; apt-get dist-upgrade (or aptitude update; aptitude
353 dist-upgrade in newer releases) and you can upgrade from a CD in a matter of
354 minutes or point apt at one of the over 300 Debian mirrors and upgrade over the
357 \rotatebox{90}{\includegraphics[height=.9\columnwidth]{distro-dev}}
358 \rotatebox{90}{Description}
360 \paragraph{Multiple architectures and kernels}
362 Currently Debian supports an impressive number of CPU architectures: alpha,
363 amd64, armel, hppa, i386, ia64, mips, mipsel, powerpc, s390, and sparc. It also
364 runs on GNU Hurd and FreeBSD kernels besides Linux, and with the debootstrap
365 utility you will be hard-pressed to find a device that can't run Debian.
367 \paragraph{Bug tracking system}
369 Debian's bug tracking system is publicly available. We don't try to hide the
370 fact that software doesn't always work the way users want. Users are encouraged
371 to submit bug reports and are notified when and why the bug was closed. This
372 system allows Debian to respond to problems quickly and honestly.
375 \ndsection{Acknowledgements}
385 \begin{multicols}{3} % 3 columns
387 \section*{The Universal Research Platform}
389 \includegraphics[width=\columnwidth]{logo_tuned/label}
390 \url{http://neuro.debian.net}
391 %\ndsection{NeuroDebian Project:}
395 \ndsection{NeuroDebian is}
397 a Debian project that provides the Neuroscience community with a
398 stable and versatile research platform -- the Debian operating system.
399 Since 2005, \mbox{NeuroDebian} integrates neuroscience software into Debian
400 to allow neuroscientists to benefit from the advantages of
401 the universal operating system in their day-to-day research activities.
402 The NeuroDebian repository
403 (\url{http://neuro.debian.net}) offers the latest research software for
404 all Debian suites (and various releases of Ubuntu).
405 The combination of a stable generic
406 operating system, Debian, and a variety of conveniently accessible research
407 software creates a versatile research platform for neuroscience that offers the
408 latest methodologies of the field to everyone, for free.
409 These advantages make NeuroDebian increasingly popular among
410 neuroscientists and scientific software developers.
414 \ndsubsection{NeuroDebian is NOT}
416 yet another Debian GNU/Linux derivative distribution. All work done
417 by the NeuroDebian project targets the official Debian operating system. This
418 approach helps to increase the longevity of the project by relying on the
419 efforts of thousands of Debian contributors.
424 \ndsubsection{Software at your fingertips}
427 \url{http://neuro.debian.net/pkgs.html}
430 \textit{Distributed computing:} Condor, DMTCP, IPython, \ldots \\
431 \textit{Electrophysiology:} BioSig, Neo, Sigviewer, \ldots\\
432 \textit{Machine Learning:} MDP, PyMVPA, sklearn, \ldots\\
433 \textit{Neural Modeling:} Brian, CNrun, PyNN, XPPAUT \ldots\\
434 \textit{Imaging:} AFNI, CMTK, FSL, Mricron, NiPy \ldots\\
435 \textit{Psychophysics:} PsychoPy, Psychtoolbox-3, PyEPL \ldots\\
438 % TODO: Environments... -- list avail cloud env using NeuroDebian
440 \ndsubsection{Benefits from Debian integration}
442 \begin{itemize}[nolistsep,leftmargin=1pc]
444 % rephrase to outline the benefit, not burden
445 \item Debian standards and policies guarantee quality and robustness.
447 \item Debian's centralized bug tracking system provides a unified
448 single-point of entry for bug reporting and troubleshooting
449 for any software in Debian.
451 \item Debian makes software available through a world-wide distribution
452 network, thus offloading bandwidth demands.
454 \item Other Debian contributors handle large-scale aspects of
455 deployment, quality assurance, porting and integration at the level
456 of the entire distribution:
458 \begin{description}[nolistsep,leftmargin=1pc]
459 \item[Porting] Software sources get built for 11 hardware
460 architectures and 3 kernels (Linux, HURD, kFreeBSD). Porter teams
461 maintain build infrastructure and help make the code
463 \item[QA] Whole-archive rebuilds assure robustness of packaging and
464 warn about upcoming problems (core libraries upgrades) beforehand.
465 \item[Internationalization (I18n)] Translator teams help localize
466 software for more than 60 languages.
469 \item Neuroscience software becomes a 1st-class citizen within the
470 Debian project, which guarantees its longevity, smooth installation
473 %\item Participation in the Debian community helps to assure Debian's
474 % aptness for the neuroscientific software demands
482 \ndsubsection{How to get NeuroDebian}
484 \textit{Debian/Ubuntu:} \url{neuro.debian.net} repository \\
485 \textit{Others:} NeuroDebian Virtual Machine
487 % Here place a left-top corner of OSX with seamless mode
489 \includegraphics[width=\columnwidth]{../shots/mac_vm_mricron}
492 \ndsubsection{Developers oriented information}
496 \ndsubsection{Who is using NeuroDebian}
499 %\includegraphics[width=\columnwidth]{usage_worldmap}
501 buga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga duga
505 \def\blank{\hspace{0em}\vspace{-1em}}
508 \ndsubsection{Work-in-progress}
509 \begin{description}[nolistsep,leftmargin=1pc,style=nextline]
510 \item[Increased coverage]
511 \textit{Electrophysiology:} Fieldtrip \\
512 \textit{Neural Modeling:} NEURON, (NEST), LFPy \\
513 \textit{Imaging:} DTI-TK, Freesurfer, XNAT, \ldots
514 % \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}
515 \item[Improved quality assurance]
516 Extended integration and regression testing\\
517 \url{http://testkraut.readthedocs.org}
518 \item[Available snapshotting service]
519 % Entire NeuroDebian repository for any given past moment
520 All versions of packages readily available
521 \item[Data as the 1st-class citizen]
522 \url{http://neuro.debian.net/datasets.html}\\
523 \url{http://github.com/neurodebian/datagit}
524 % yoh: see TODO above -- we can say that it is available already
525 %\item[Universal availability]
526 % % \begin{itemize}[nolistsep,leftmargin=1pc,topsep=0em]
527 % % \item Virtual Appliance enhancements
534 \ndsubsection{Testimonials}
537 \url{http://neuro.debian.net/testimonials.html}
541 % TODO yoh: This one remains the best summary IMHO. But may be
542 % we would just kick this section out an place Testimonials into References
543 \epigraph{The approach taken with NeuroDebian is plainly the most appropriate
544 approach to software distribution for the dominant platform in brain
545 image analysis, and I have great confidence that this project will be
546 a major asset to the neuroscience community in facilitating the
547 distribution of stable software, improving the reliability and
548 replicability of analyses, and in helping to improve software
549 development practices.}{Prof. Daniel Y. Kimberg}{Director, Data
550 Processing Facility, Center for Functional Neuroimaging, University of
551 Pennsylvania, Philadelphia, USA}
553 \ndsubsection{Acknowledgements}
555 NeuroDebian is grateful to all Debian developers and contributors for
556 developing the Debian operating system, to
557 \href{http://www.incf.org}{INCF} for the support in community outreach
558 and technical collaborations, and to
559 Prof. \href{http://haxbylab.dartmouth.edu}{James V. Haxby}
560 (\href{http://www.dartmouth.edu/~psych}{PBS Department, Dartmouth
561 College}) for his continued support and endless supply of Italian
562 espresso (\url{http://neuro.debian.net/coffeeart.html}).
565 \ndsubsection{References}
567 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.
569 % TODO: adjust for the new layout
570 \url{http://neuro.debian.net/#publications}
584 %%% whizzy-viewers: (("-pdf" "okular") ("-dvi" "xdvi") ("-ps" "gv"))