[Cdd-commits] r1167 - projects/med/trunk/papers/09_osehc_porto

CDD Subversion Commit noreply at alioth.debian.org
Tue Oct 28 22:53:40 UTC 2008

Author: tille
Date: Tue Oct 28 22:53:39 2008
New Revision: 1167

   projects/med/trunk/papers/09_osehc_porto/earthkeyring.png   (contents, props changed)
Inject rough draft of paper for OSEHC 2009 which is based on BIOMED 05 paper.  Deadline is 31. October = *very* short.  Any hint is welcome.

Added: projects/med/trunk/papers/09_osehc_porto/Makefile
--- (empty file)
+++ projects/med/trunk/papers/09_osehc_porto/Makefile	Tue Oct 28 22:53:39 2008
@@ -0,0 +1,101 @@
+#!/usr/bin/make -f
+%.html: %.tex
+	echo "Unfortunately there is no latex 2 html solution for the moment."
+all: pdf
+# html dvi
+html: $(text).html
+$(text).html: $(text).tex
+	make clean
+	make bbl
+	cp -a $(text).tex $(text).tex.save
+	sed -i \
+	    -e "s/\(\\documentclass{\)acm_proc_article-sp/\1article/" \
+	    -e "s/\(\\\\titlenote{.*\)\\\\printurl{[^}]*}{[^}]*}/\1/" \
+	    -e "/\\\\titlenote{/{;N;N;s/\\\\titlenote{[^}]*}//;}" \
+	    -e "/\\\\affaddr{.*}/d" \
+	    -e "/\\\\email{.*}/d" \
+	    -e "/\\\\alignauthor/d" \
+	    -e "/\\\\numberofauthors/d" \
+	    $(text).tex
+	sed -i \
+	    -e "/\\\\author{/{;N;N;N;N;N;N;N;N;s/\\\\author{[^}]*}//;}" \
+	    -e "s/\\\\halfsloppy//" \
+	    -e "/\\\\printurl/{;N;N;s?\\\\printurl{\([^}]*\)}\({[^}]*}\)?\\\\htmladdnormallink\2{http://\1}?g;}" \
+	    -e "s/\(\\\\begin{tabular}{.*\)p{[^}]*}\(.*\)/\1l\2/" \
+	    -e "/\\\\conferenceinfo/{;N;N;s/\\\\conferenceinfo{[^}]*}{[^}]*}/\\\\htmladdnormallink{Find the paper in PDF and more information about the conference here}{..}/;}" \
+	    -e "s/\\\\CopyrightYear{[^}]*}//" \
+	    $(text).tex
+	sed -i \
+	    -e "/\\\\ifshowURL/{;N;N;N;s?\\\\ifshowURL.*|\(http://[^,]*\)[[:space:],]*\(http://[^|]*\)|}\\\\fi?\\\\htmladdnormallink{\1}{\1}, \\\\htmladdnormallink{\2}{\2}?g;}" \
+	    $(text).bbl
+	sed -i \
+	    -e "/\\\\ifshowURL/{;N;N;N;s?\\\\ifshowURL.*|\(http://[^|]*\)|}%*[[:space:]]*\\\\fi?\\\\htmladdnormallink{\1}{\1}?g;}" \
+	    $(text).bbl
+	sed -i \
+	    -e "/\\\\ifshowURL/{;N;N;s?\\\\ifshowURL.*|\(http://[^|]*\)|}%*[[:space:]]*\\\\fi?\\\\htmladdnormallink{\1}{\1}?g;}" \
+	    -e "/\\\\htmladdnormallink/s/%/\\\\%/g" \
+	    $(text).bbl
+	sed -i \
+	    -e "/\\\\ifx[[:space:]]\\\\.*[[:space:]]\\\\fi/d" \
+	    $(text).bbl
+	latex2html -local_icons $(text).tex
+	touch $(text).html
+	##mv $(text).tex $(text).tex_used4html
+	mv $(text).tex.save $(text).tex
+bbl: $(text).bib
+	pdflatex $(text).tex
+	bibtex debian-med-bio
+dvi: $(text).dvi
+$(text).dvi: $(text).tex
+	make clean
+	convert earthkeyring.png earthkeyring.eps
+	latex $(text).tex
+	bibtex $(text)
+	latex $(text).tex
+	latex $(text).tex
+pdf: $(text).pdf
+$(text).pdf: $(text).tex paper-text.tex $(text).bib
+	make clean
+	pdflatex $(text).tex
+	bibtex $(text)
+	pdflatex $(text).tex
+	pdflatex $(text).tex
+pdfllncs: $(text)-llncs.pdf
+$(text)-llncs.pdf: $(text)-llncs.tex paper-text.tex
+	make clean
+	pdflatex $(text)-llncs.tex
+	bibtex $(text)-llncs
+	pdflatex $(text)-llncs.tex
+	pdflatex $(text)-llncs.tex
+dvips: $(text)-dvips.pdf
+$(text)-dvips.pdf: $(text).dvi
+	dvips -o $(text)-dvips.ps $(text).dvi
+	ps2pdf $(text)-dvips.ps
+	rm $(text)-dvips.ps
+distclean: clean
+	rm -f $(text)*.html $(text).pdf $(text)-dvips.pdf $(text)-llncs.pdf
+	rm -rf $(DISTDIR) debian-med-bio
+	rm -f $(text)*.log $(text)*.aux $(text)*.dvi $(text)*.toc $(text)*.out $(text)*.bbl $(text)*.blg
+	rm -f *.log
+	rm -f earthkeyring.eps
+	mkdir -p $(DISTDIR)/paper
+	cp -a *.tex *.css Makefile $(DISTDIR)/paper
+	tar -czf $(DISTDIR).tgz $(DISTDIR)
+	rm -rf $(DISTDIR)

Added: projects/med/trunk/papers/09_osehc_porto/debian-med-bio.bib
--- (empty file)
+++ projects/med/trunk/papers/09_osehc_porto/debian-med-bio.bib	Tue Oct 28 22:53:39 2008
@@ -0,0 +1,277 @@
+ at ARTICLE{bar:openmosix,
+	AUTHOR = "M. Bar and B. Knox",
+	TITLE = "OpenMosix: The Other Kind of HPC Cluster",
+	JOURNAL = "ClusterWorld",
+	VOLUME = {2},
+	NUMBER = {12},
+	YEAR = {2004},
+        URL = {http://www.openmosix.org}
+	}
+ at ARTICLE{eddelbuettel:quantian,
+	AUTHOR = "Dirk Eddelbuettel",
+	TITLE = "Quantian: A Scientific Computing Environment",
+	JOURNAL = {Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003)},
+	VOLUME = {12},
+	NUMBER = {2},
+	PAGES = {291-301},
+	MONTH = "March",
+	YEAR = {2003},
+        URL  = {http://dirk.eddelbuettel.com/quantian},
+        note = {Vienna, Austria},
+        editors = "Hornik K., Leisch F., Zeileis A." 
+	}
+ at ARTICLE{dfsg,
+        AUTHOR = "Bruce Perens and Ean Schuessler and Debian",
+	TITLE = "Debian Free Software Guidelines",
+	ORGANIZATION = "Debian",
+	MONTH = "June",
+	YEAR = {1997},
+        URL = {http://www.debian.org/social_contract#guidelines}
+	}
+ at INPROCEEDINGS{tille:ltk03,
+	AUTHOR = "Andreas Tille",
+	TITLE = "Freie Software im Gesundheitswesen",
+        BOOKTITLE = "Proceedings LinuxTag 2003",
+        ORGANIZATION = "LinuxTag",
+	MONTH = "July",
+	YEAR = {2003},
+        URL  = {http://people.debian.org/%7Etille/talks/200307_ltk/paper-305-de.html}
+	}
+ at ARTICLE{tille:cdd,
+	AUTHOR = "Andreas Tille",
+	TITLE = "Custom Debian Distributions",
+        ORGANIZATION = "Debian",
+	MONTH = "June",
+	YEAR = {2004},
+        URL  = {http://people.debian.org/%7Etille/cdd}
+	}
+ at INPROCEEDINGS{eerola:2004,
+	AUTHOR = "P. Eerola and T. Ekelöf and M. Ellert and J.R. Hansen and A. Konstantinov and B. Konya and J.L. Nielsen and F. Ould-Saada and O. Smirnova and A. Wäänänen",
+	TITLE = "Science on NorduGrid",
+	YEAR = "2004",
+        URL = {http://www.nordugrid.org/documents/eccomas04.pdf}
+	}
+ at ARTICLE{foster:2001,
+	AUTHOR="Foster I., Kesselman C., Tuecke S.",
+	YEAR=2001,
+	TITLE="The Anatomy of the Grid: Enabling Scalable Virtual Organizations.",
+	JOURNAL="International J. Supercomputer Applications",
+	VOLUME=15,
+ at ARTICLE{hubbard:2005,
+	AUTHOR="T. Hubbard and D. Andrews and M. Caccamo and G. Cameron and Y. Chen and M. Clamp and L. Clarke and G. Coates and T. Cox and F. Cunningham and V. Curwen and T. Cutts and T. Down and R. Durbin and X.M. Fernandez-Suarez and J. Gilbert and M. Hammond and J. Herrero and H. Hotz and K. Howe and V. Iyer and K. Jekosch and A. Kahari and A. Kasprzyk and D. Keefe and S. Keenan and F. Kokocinsci and D. London and I. Longden and G. McVicker and C. Melsopp and P. Meidl and S. Potter and G. Proctor and M. Rae and D. Rios and M. Schuster and S. Searle and J. Severin and G. Slater and D. Smedley and J. Smith and W. Spooner and A. Stabenau and J. Stalker and R. Storey and S. Trevanion and A. Ureta-Vidal and J. Vogel and S. White and C. Woodwark and E. Birney",
+	TITLE="Ensembl 2005.",
+	JOURNAL="Nucleic Acids Res.",
+	YEAR=2005,
+	VOLUME=33,
+	PAGES="D447-D453"
+ at ARTICLE{stevens:2004,
+	AUTHOR="R. Stevens and H.J. Tipney and C. Wroe and T. Oinn and M. Senger and P. Lord and C.A. Goble C.A. and A. Brass and M. Tassabehji",
+	TITLE="Exploring Williams-Beuren Syndrome Using myGrid",
+	YEAR=2004,
+	ADDRESS="Glasgow, UK",
+	JOURNAL="Bioinformatics",
+	VOLUME=20,
+	NUMBER="Suppl. 1",
+	PAGES="i303-i310",
+	URL="http://www.mygrid.org.uk"
+ at article{wilkinson:2005,
+	AUTHOR="M. Wilkinson and H. Schoof and R. Ernst and D. Haase",
+	YEAR=2005,
+	TITLE="BioMOBY successfully integrates disributed heterogenous bioinformatics web services. The PlaNet exemplar case.",
+	JOURNAL="Plant Physol.",
+	VOLUME=138,
+	PAGES="1-13"
+ at ARTICLE{zdobnow:2002,
+	AUTHOR="E.M. Zdobnov and R. Lopez and R. Apweiler and T. Etzold",
+	TITLE="The EBI SRS server-new features.",
+	JOURNAL="Bioinformatics",
+	YEAR=2002,
+	VOLUME=18,
+	PAGES="1149-1150",
+	URL="http://srs.ebi.ac.uk"
+ at INPROCEEDINGS{lord:2004,
+	AUTHOR="P. Lord and S. Bechhofer and M.D. Wilkinson and G. Schiltz and D. Gessler and D. Hull and C. Goble and L. Stein",
+	YEAR=2004,
+	TITLE="Applying semantic web services to Bioinformatics: Experiences gained, lessons learnt",
+	PUBLISHER="Springer-Verlag Berlin Heidelberg",
+	PAGES="350-364"
+ at INPROCEEDINGS{merelli:2002,
+	AUTHOR="E. Merelli and L. Culmone and L. Mariani",
+	TITLE="BioAgent: A Mobile Agent System for Bioscientists",
+	BOOKTITLE="NETTAB02 Agents in Bioinformatics, Bologna",
+	YEAR="2002",
+	URL="http://www.bioagent.net"
+ at ARTICLE{fink:2005,
+	AUTHOR="Fink Development Team",
+	TITLE="Fink",
+	YEAR="2005",
+	URL="http://fink.sourceforge.net"
+ at ARTICLE{hess:2003,
+	AUTHOR="Joe Hess",
+	TITLE="Comparing Linux/UNIX Binary Package Formats",
+	YEAR="2003",
+	URL="http://www.kitenet.net/%7Ejoey/pkg-comp"
+ at ARTICLE{knopper:2005,
+	AUTHOR="Klaus Knopper",
+	TITLE="Knoppix Live CD",
+	YEAR="2005",
+	URL="http://www.knopper.net"
+ at ARTICLE{kojima:2000,
+	AUTHOR="Alfredo K. Kojima",
+	TITLE="An RPM port of APT",
+	YEAR="2000",
+	URL="http://freshmeat.net/articles/view/192 , http://apt4rpm.sourceforge.net"
+ at ARTICLE{larsen:2005,
+	AUTHOR="Niels E. Larsen",
+	TITLE="ARC Knoppix",
+	YEAR="2005",
+	URL="http://cvs.nordugrid.org/knx/arcknoppix.iso"
+ at ARTICLE{larsenscript:2005,
+	AUTHOR="Niels E. Larsen",
+	TITLE="Script to add the NorduGrid to the basic Knoppix distribution",
+	YEAR="2005",
+	URL="http://cvs.nordugrid.org/mkknx"
+ at ARTICLE{lsb,
+	AUTHOR="LSB Workgroup",
+	TITLE="Linux Standard Base",
+	YEAR="2005",
+	URL="http://www.linuxbase.org"
+ at ARTICLE{mysql,
+	YEAR="2005",
+	URL="http://www.mysql.com"
+ at ARTICLE{debianpolicy,
+	AUTHOR="Ian Jackson and Christian Schwarz and Debian",
+	TITLE="Debian Policy Manual ",
+	YEAR="2005",
+	URL="http://www.debian.org/doc/debian-policy"
+ at ARTICLE{vandersmissen:2005,
+	AUTHOR="W. Vandersmissen",
+	TITLE="Clusterknoppix",
+	YEAR="2005",
+	URL="http://bofh.be/clusterknoppix"
+ at ARTICLE{myers:2003,
+	AUTHOR="Daniel S. Myers and Michael P. Cummings",
+	TITLE="Necessity is the mother of invention: a simple grid computing system using commodity tools",
+	JOURNAL="Journal of Parallel and Distributed Computing",
+	Volume=63,
+	YEAR=2003,
+	Pages="578-589",
+	URL="http://lattice.umiacs.umd.edu"
+ at INPROCEEDINGS{anderson:2004,
+	AUTHOR="David P. Anderson",
+	TITLE="BOINC: A System for Public-Resource Computing and Storage",
+	BOOKTITLE="5th IEEE/ACM International Workshop on Grid Computing",
+	YEAR=2004,
+	ADDRESS="Pittsburgh, USA",
+	URL="http://boinc.berkeley.edu"
+ at article{Wheeler2005,
+	author="DL Wheeler and T. Barrett and DA Benson and SH Bryant and K. Canese and DM Church and M. DiCuccio and R. Edgar and S. Federhen and W. Helmberg and DL Kenton and O. Khovayko and DJ. Lipman and TL Madden and DR Maglott and J. Ostell and JU Pontius and KD Pruitt and GD Schuler and LM Schriml and E. Sequeira and ST Sherry and K. Sirotkin and G. Starchenko and TO Suzek and R. Tatusov and TA Tatusova and L. Wagner and E. Yaschenko",
+	title="Database resources of the National Center for Biotechnology Information.",
+	journal="Nucleic Acids Res.",
+	year=2005,
+	volume=33,
+	number="1 (Database issue)",
+	Pages="D39-D45"
+ at article{Jenuth2000,
+	author="JP. Jenuth",
+	title="The NCBI. Publicly available tools and resources on the Web.",
+	journal="Methods Mol. Biol.",
+	year=2000,
+	volume=132,
+	pages="301-312"
+ at article{ncbi:2004,
+	author="NCBI",
+	title="The NCBI C++ Toolkit book.",
+	year=2004,
+	URL="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit.chapter.ch_datamod"
+ at article{Bellifemine2001,
+	title="Developing multi-agent systems with a FIPA-compliant agent framework",
+	author="Fabio Bellifemine and Agostino Poggi and Giovanni Rimassa",
+	booktitle="Software - Practice And Experience",
+	year=2001,
+	volume=31,
+	pages="103-128"
+ at ARTICLE{wikipediaoslist:2008,
+	AUTHOR="Wikipedia",
+	TITLE="List of open source healthcare software",
+	YEAR="2008",
+	URL="http://en.wikipedia.org/wiki/List_of_open_source_healthcare_software"
+ at ARTICLE{openvista:2008,
+	AUTHOR="OpenVista",
+	TITLE="Enterprise grade health care information system developed by the U.S. Department of Veterans Affairs (VA)",
+	YEAR="2008",
+	URL="http://sourceforge.net/projects/openvista"
+ at ARTICLE{bioimagesuite:2008,
+	AUTHOR="Yale University",
+	TITLE="BioImageSuite an integrated image analysis software suite",
+	YEAR="2008",
+	URL="http://www.bioimagesuite.org/"
+ at ARTICLE{gnumed:2008,
+	AUTHOR="Karsten Hilbert",
+	TITLE="GNUmed",
+	YEAR="2008",
+	URL="http://www.gnumed.org/"

Added: projects/med/trunk/papers/09_osehc_porto/debian-med-bio.tex
--- (empty file)
+++ projects/med/trunk/papers/09_osehc_porto/debian-med-bio.tex	Tue Oct 28 22:53:39 2008
@@ -0,0 +1,90 @@
+% debian-med-bio.tex
+% Author: Andreas Tille
+% Revisions: 28 October 2008
+  \pdffalse % we do not use PDFLaTeX
+  \PassOptionsToPackage{dvips}{graphics}
+  \pdfoutput=1 % we use PDFLaTeX
+  \pdftrue
+  \PassOptionsToPackage{pdftex}{graphics}
+  \PassOptionsToPackage{pdftex,colorlinks=true,urlcolor=blue,linkcolor=blue}{hyperref}
+  \pdfcompresslevel=9
+  \usepackage{url}
+%\usepackage[english]{babel} %%% conflicts with \cite !!!
+   \ifpdf
+   \href{mailto:#1}{$<$#1$>$}%
+   \else
+   \onlynameurl{$<$#1$>$}%
+   \fi
+   \xspace
+   \htmladdnormallink{#2}{http://#1}%
+%   \ifpdf
+%   \htmladdnormallink{#2}{http://#1}%
+%   \else
+%   \onlynameurl{#2}%
+%   \fi
+   \xspace
+   \ifpdf
+   % \resizebox{#2}{#3}{%
+   %\resizebox{80mm}{53mm}{%
+      \includegraphics{#1}%
+   %}%
+   \else
+      \includegraphics{#1}%
+      %%\epsfig{file=#1.eps}%, height=#2, width=#3} 
+   \fi
+  \tolerance 1250%
+  \emergencystretch 0.75em}
+\date{31 October 2008}
+% http://www.biostec.org/OSEHC.htm
+% --- Author Metadata here ---
+\title{Debian Med \\
+       Integrated software environment for all medical purposes based on Debian GNU/Linux}
+%%% Bug in style: \titlenote creates extra page :-(
+\author{Andreas Tille}
+%\email{tille at debian.org}
+\input paper-text

Added: projects/med/trunk/papers/09_osehc_porto/earthkeyring.png
--- (empty file)
+++ projects/med/trunk/papers/09_osehc_porto/earthkeyring.png	Tue Oct 28 22:53:39 2008
@@ -0,0 +1 @@
+link ../05_biomed_bio/earthkeyring.png
\ No newline at end of file

Added: projects/med/trunk/papers/09_osehc_porto/paper-text.tex
--- (empty file)
+++ projects/med/trunk/papers/09_osehc_porto/paper-text.tex	Tue Oct 28 22:53:39 2008
@@ -0,0 +1,790 @@
+\newcommand{\DebianMed}{Debian\ Med\xspace}
+  The Debian Med project started in 2002 with the objective to bring
+  free medical software into the focus of users. The first step was
+  the investigation of available Free Software in this area and to
+  accomplish the conditions for a simple and solid installation of
+  this software in Debian GNU/Linux.  It has shown that the Debian Med
+  project has a positive effect for the cooperating upstream projects.
+  It has shown that fields like molecular biology and medical imaging
+  were covered quite good with Free Software solutions while there is
+  not really much to manage a medical practice. The Debian Med project
+  tries to be the missing link between developers and users to support
+  Free Software solutions for all areas in medicine.
+  Debian Med is intended to be useful for service providers who want
+  to distribute their free or proprietary solutions in medical care.
+  The whole project is embeded into the Debian Pure Blends framework
+  (formerly known as Custom Debian Distributions) as well as Debian
+  Edu, Debian Science and others.
+\begin{tabular}{ll} % to become llll later
+Blend&Debian Pure Blend \\
+BTS&  Bug Tracking System \\
+DFSG& Debian Free Software Guidelines \\
+LSB&  Linux Standard Base \\
+\subsection{Motivation and purpose of \DebianMed}
+The advent of \DebianMed is characterised by the rise of several new
+Free Software projects that were useful for certain tasks in medical
+care.  Several of these projects -- even if looking promising in the
+beginning -- do not really exist any more because they did not
+respected the principle of Free Software: care for a solid user base
+and recruit qualified developers from it.  This task is one of the
+hardest in the field of health care: there is a much smaller number of
+users for such specific software compared to a web browser or an
+office suite.
+A big problem was that it was quite hard to obtain solid information
+about all these projects.  Some engaged users tried to assemble lists
+of these projects and published these in the web.  While those lists
+are an interesting start they are finally not really helpful for
+users: Users just need ready to run programs with no effort to obtain
+and install the software.  The idea of \DebianMed was now to provide
+not only a list but exactly what users need.
+\subsection{Status of Free Software in health care}
+Common programs like a web server, or a mail user agent are installed
+on most computers and have a very large user base.  Knowing this, many
+gifted programmers feel obliged for this kind of Free Software - they
+just need it for their own and they know to make a difference to the
+world.  So one finds a fast, growing community around Free Software
+packages that have a widespread use.  For specialised software in
+general and particularly for biological software, one needs to first
+explain what a particular software does. Often the developers get
+their satisfaction not from the software but from the excitement of
+extra insights in biological processes - the beauty of which is likely
+not to be accessible to regular software enthusiasts.
+Considering the fact that an important part of medical care is based
+on microbiology and genetic analysis this software forms one important
+column of the \DebianMed project.  As a view shared by many in Open
+Source Bioinformatics, Ewan Birney of the EnsEMBL \cite{hubbard:2005}
+project stresses Open Source to "ensure scientific progress".  He also
+laid out that the Open Source of programs is a comparatively trivial
+issue when compared with the openness of biological data. The latter
+is often far more expensive to produce. While giving the data away
+might possibly diminish one's competitive advantage, the sharing of a
+program with others and respective citations is well accepted as
+fostering one's career.  This is one reason for the fact that today
+the field of microbiology is well covered by Free Software and the
+most important ones are now packaged for Debian.
+Another quite well covered part of \DebianMed is medical imaging.
+Even if there are quite important packages like Bio Image Suite
+\cite{bioimagesuite:2008} not yet packaged for Debian first steps are
+done and there is a certain coverage of DICOM viewers and other
+software which is very useful in medical imaging.
+It has shown that the field of patient management and medical health
+record applications which is considered by most people as the basic
+health care software has only one single representative which is
+GNUmed \cite{gnumed:2008}.  It has turned out that there are a lot of
+similar Free Software projects that try to solve more or less the same
+problem but diverge in the techniques used (programming language,
+database server, etc.), user interface (GUI or web aplication) and the
+basic ideas about workflow and philosophy.
+The even larger task to manage a hospital is also tackled by several
+projects and the most famous one OpenVista\cite{openvista:2008} as a
+real enterprise grade health care information system is a really
+complex project and needs a stronger team than the current \DebianMed
+team with a larger technical background in the specific techniques
+used in OpenVista.  To overcome this problem the strategy of
+\DebianMed is to try to involve the upstream authors into the
+packaging: They are really the experts of the software in question and
+we try to teach and help them in packaging.
+\subsection{Unique technology supporting Debian's principles in packaging}
+\subsubsection{{\ttfamily .deb} packages}
+Most distributors ship their distribution in binary packages.  Two
+package formats are widely used\cite{hess:2003}:
+\item[RPM (RedHat Package Manager)] which is supported by RedHat,
+  SuSE, Mandrake and others.
+\item[DEB (Debian Package)] used by Debian and derived distributions.
+It is this {\itshape adherence to policy\/} that causes a distribution
+to remain consistent within its own bounds. At the same time, this is
+the reason why packages can not always be safely installed across
+distribution boundaries. A SuSE \file{package.rpm} might not play well
+with a RedHat \file{package.rpm}, although the packages work perfectly
+well within their own distributions. A similar compatibility problem
+could also apply to packages from the same distributor, but from a
+different version or generation of the distribution.
+For Debian, all files of a program are packed as the \command{ar}
+archiver, otherwise known for the creation of programming libraries.
+Every such DEB package has a companion source package from which the
+binary package may be built automatically.  The distributions of SuSE,
+RedHat and derivatives use the RPM format.  The program
+\command{alien} by Joey Hess can translate between these. Though
+scripts to be run upon installation may get lost in the translation
+\subsubsection{Build daemons}
+Sites external to the Debian main distribution may 
+offer packages only for a subset of architectures.
+The Debian main distribution, however, automatically
+compiles software for all 11 
+architectures that are supported by the Debian effort.
+To get a package into Debian, be it novel or an update of an existing package,
+the maintainer of a package submits the source code of the program together with his changes on the code to create the package. The build daemons (or autobuilders) compile the packages for each of the supported systems and make the resulting package publicly available for download. Logs of the build platforms are available online for everybody's inspection.
+\subsubsection{Bug tracking system}
+Users should give immediate feedback about problems arising in using a
+package.  They always have the choice of reporting these to the
+upstream developer, usually per email. A particular strength of
+\printurl{www.sourceforge.net}{SourceForget.net} is to bring users of
+a particular software together.  Earlier than this effort was the
+\printurl{www.debian.org/Bugs}{Debian Bug Tracking System} (BTS).
+The maintainer of a software can decide if the bug should be forwarded to the upstream
+developers of the package or if it is fixed by himself. All problems are made
+public and hence the whole community may contribute to solving a particular issue.
+\subsection{Divide and conquer of package maintenance}
+The Debian Project is an association of individuals who share the
+intention to create the best possible free operating system.  This
+operating system that which is created is called Debian GNU/Linux, or
+simply Debian for short.  Everybody in the internet may initiate a site
+and offer packages for the installation in Debian. A local administrator
+has to decide, if this public source may be trusted.
+For Free Software development to work it requires a critical mass of
+supporters. Development without feedback prior to the submission of the
+final product is disadvantageous.  The development of programs is not the
+main concern of a regular Linux Distribution.  However, with the focus
+on Free Software and smooth local compilation, Debian considerably eases
+the contribution of comments and concise feedback of the technically skilled
+early adopters. Debian such helps to bring developers and users of
+applications together.
+\caption{Debian web of trust}\label{figure:weboftrust}
+All members of the Debian project are connected in a
+\printurl{people.debian.org/~edward/globe/earthkeyring}{web of trust},
+which is woven by signing GnuPG
+(\printurl{www.gnupg.org}{www.gnupg.org}) keys\ref{figure:weboftrust}.
+A central requirement to become a member of the Debian project is to
+have one's GPG key signed by an already accepted member of the Debian
+community.  When Debian developers first meet in person, they sign
+each other's keys.  Thus, the web of trust is woven.
+Debian does its best to have every member profit of somebody else's work as quickly as possible.
+\subsubsection{Debian Policy}
+All GNU/Linux distributions have a certain amount of common ground,
+and the \printurl{www.linuxbase.org/}{Linux Standard Base}
+(LSB)\cite{lsb} is attempting to develop and promote a set of
+standards that will increase compatibility among Linux distributions,
+hereby enabling software applications to run on any compliant system.
+The very essence of any distribution, (whether delivered as RPMs,
+DEBs, Source tarballs or ports) is the choice of {\itshape policy
+  statements\/}.
+\halfsloppy{\itshape Policy statements\/} in Debian\cite{debianpolicy}
+specify configuration files to reside in
+\Path{/etc/\$package/\$package.conf}, logfiles go to
+\Path{/var/log/\$package/\$package.log} and the documentation files to
+be located in \Path{/usr/share/doc/\$package}.  CGI-scripts are
+installed in \Path{/usr/lib/cgi-bin}.
+The policy statements are followed by the tool-chains and
+libraries used to build the software, and the lists of dependencies, which
+dictate the prerequisites and order in which the software has to be
+built and installed.
+Policies in Debian are developed within the community. Commonly with
+a single person or a small team drafting it, with further refinements
+being discussed in respective mailing lists.
+While every single maintainer of a Debian package has to build the
+package in compliance with the policy he has the ability and the right
+to decide which software is worth packaging.  Normally maintainers
+choose the software which is used in their own work and they are free
+to move the development of Debian in a certain direction (as long as
+they follow the rules of the policy).  This is referred to as {\em
+  Do-o-cracy} in Debian which means: The doer decides what is done.
+\subsection{Selection of packages}
+Debian contains nearly 10000 binary packages, and this number is
+constantly increasing.  There is no single user who needs all these
+packages.  The regular user is interested in a subset of these packages.
+To specify packages of one's particular interest, several options are
+provided by Debian:
+  Provision of a reasonable selection of rather general tasks that can
+  be accomplished using a set of packages installed on a Debian
+  GNU/Linux system.  However, these are not yet covering scientific
+  applications. The CDD toolkit which is currently developed will also
+  support \command{tasksel} to enable selecting for instance
+  Debian Med right after a fresh installation of a general Debian
+  system.
+\item[standard package management]
+  \command{dpkg} and \command{apt} provide means to search for
+  packages of particular interest by its name or words in the
+  package's description. Every package also indicates, as set by its
+  maintainer, references to other packages of potential interest.
+In its current development, an ontology of applications of software,
+upon which semantical queries could be performed, analogous to 
+Moby-S and \printurl{www.biomoby.org}{BioMoby} \cite{lord:2004,wilkinson:2005}
+effort, is not available.
+A package management system is a very strong tool to manage software
+packages on your computer. A large amount of the work of a
+distributor is building these software packages.
+The Debian package management tools have been ported to
+MacOS X\cite{fink:2005} and other Linux Distributions\cite{kojima:2000}.
+Debian officially maintains 11 different architectures with many more
+not officially supported ports to other operating systems, which includes some
+that run another flavour of UNIX. Its
+technology for package management has been adopted for other operating
+systems, i.e. Fink on MacOSX
+A {\itshape distribution\/} is a collection of software packages around the
+GNU Linux operating system that satisfies the needs of the target user
+group.  There are general distributions, which try to support all
+users, and there are several specialised distributions, which each
+target a special group of users.
+{\itshape Distributors\/} are those companies that are building these
+collections of software around the GNU Linux operating system.
+Since the software is Free, the user who buys a distribution pays for
+the service that the distributor is providing.  These services might
+  \item Preparing a useful collection of software around GNU Linux.
+  \item Caring for smooth installation that the target user is able to
+    manage.
+  \item Providing software updates and security fixes.
+  \item Writing documentation and translations to enable the user to
+    use the distribution with maximum effect.
+  \item Selling Boxes with ready to install CDs and printed
+    documentation.
+  \item Offering training and qualification.
+The best established Distributors of GNU/Linux systems are
+\printurl{www.redhat.com}{RedHat}, \printurl{www.suse.com}{SuSE} (now
+owned by \printurl{www.novell.com/linux}{Novell}) and
+\printurl{www.mepis.org}{MEPIS} and
+\printurl{www.ubuntulinux.org}{Ubuntu} are well known derivates of
+\subsection{Bioinformatics and Debian-associated repositories}
+\item[Bio-Linux Bioinformatics package repository]
+  \halfsloppy The Bio-Linux Bioinformatics package repository contains
+  the \printurl{envgen.nox.ac.uk/pkg\_repository.html}{Bio-Linux 4
+    bioinformatics software} and can be installed from a centralised
+  repository located on the EGTDC server.  The packages available from
+  this site have been created by the EGTDC specifically for the
+  Bio-Linux project and are in deb format.
+  The projects claim to be compatible with any installation of Debian
+  or Debian variants.  This might be a weak sentence because Debian
+  variants are quite different.  It is better to say exactly Debian
+  "stable" or Debian "testing" and draw a line between native Debian
+  and perhaps commercial derivatives which might differ in certain
+  aspects.
+  The packages are not, however, core Debian packages. Please read the
+  notes below for further details about Bio-Linux packages.  They add
+  the following notes:
+  \begin{enumerate}
+  \item \sloppy {\em All} of the packages have a dependency on the package
+    \package{bio-linux-base-directories}, as this is the package that
+    sets up the directory structure and dependencies of several of the
+    Bio-Linux system packages.  This creates a number of directories
+    and configuration files for Bio-Linux but will NOT overwrite
+    anything on your system.  Therefore you may wish to install this
+    package first, or force the install of other packages if you do
+    not want to install this package.
+  \item {\em Warning}: The \package{bio-linux-bldp-files} package
+    contains files which install to a folder called
+    \Path{/var/www/boinformatics}.  Thus, please ensure that you do
+    not already have a directory on your system of this name, or that,
+    at the very least, you are not concerned with overwriting any
+    index.html file in such an existing directory.
+  \item All packages install to \Path{/usr/local/bioinf} and create
+    symlinks in \Path{/usr/local/bin} with the exception of the
+    bio-linux-genespring software which installs to
+    \Path{/home/db/SiliconGenetics} (for more information regarding
+    installation of GeneSpring, see our
+    \printurl{envgen.nox.ac.uk/sg.html}{GeneSpring Web Page}.)
+  \item \halfsloppy \package{Bio-linux-base-directories} installs two
+    files into \Path{/usr/local/bioinf/config\_files} (\Path{bioenvrc}
+    and \Path{aliasrc}).  The file {\em \Path{bioenvrc} should be
+      sourced\/} by your shell if you want to pick up the correct
+    environmental variables for the software. We recommend the use of
+    the
+    \printurl{envgen.nox.ac.uk/envgen/software/archives/000499.html\#shells}{z-shell
+      for Bio-Linux}. You will also want to \command{source aliasrc}
+    if you wish to run some of the Java based software - for example
+    \command{maxdView}, \command{maxdLoad2}, \command{mesquite},
+    \command{forester}, etc.  You will {\em also need to edit} the
+    \Path{aliasrc} file to reflect the location of the Java binaries
+    on your system.
+  \end{enumerate}
+  The authors did a great job in collecting a certain amount of very
+  useful software for biologists and the \DebianMed project might try
+  to include some packages which are not yet available in Debian
+  officially.
+\item[BioLinux-BR Project]
+  \halfsloppy A similar project is the
+  \printurl{biolinux.df.ibilce.unesp.br/index.en.php}{BioLinux-BR
+    Project} which is a project directed to the scientific community.
+  Their goal is to create a Linux distribution for people with little
+  familiarity with the installation of the operational system and
+  mainly for people who do not know to proceed unpacking a program,
+  compile and install it correctly.
+  For these reasons, they want to give contribution, developing a
+  Linux system that aims to be easy to use and still offering packages
+  that will be part of the BioLinux-BR. Giving this option, we will
+  not be compelling anybody to change its Linux distribution, since
+  there are packages developed for the greater Linux distributions.
+  "BR" here stands for "Brasil" which might lead to the assumption
+  that some internationalisation effort was done, but according to the
+  authors this was not their main concern but rather a side effect.
+  In fact, this project has assembled a huge amount of packages,
+  probably the most complete collection of Free Software in biology.
+  Packages for multiple distributions are provided, which includes
+  Debian, and a live CD.
+  Debian developer Matt Hope has created a small set of packages for
+  Debian that he has not yet uploaded to the main distribution.
+  Most are in a very nice state he just should submit.
+\subsection{Bioinformatics Live CDs}
+The concept of a live CD allows to create a CD or DVD that boots a
+computer, starts a defined set of application without a user's
+intervention and has all tools in place that suits a particular
+community.  Such provide fully featured Linux workstations without
+additional installations of access to local disk space, alternatively
+booting via the network is supported by Debian, which particularly
+appeals to Blades or large clusters. The most successful such LiveCD
+is the Debian-derived Knoppix\cite{knopper:2005}.
+\item[The Quantian Scientific Computing Environment]
+  Quantian is a remastering of a well established effort
+  (\printurl{www.knopper.net/knoppix/index-en.html}{Knoppix}).  Recent
+  versions of Quantian \cite{eddelbuettel:quantian} are based on
+  \printurl{bofh.be/clusterknoppix/}{ClusterKnoppix
+  }\cite{vandersmissen:2005} and add support for
+  \printurl{www.openmosix.org}{OpenMosix} \cite{bar:openmosix},
+  including remote booting of light clients in an openMosix terminal
+  server context. Earlier releases are still available; see below for
+  URLs for downloads as well as ordering information.  More detailed
+  information \printurl{dirk.eddelbuettel.com/quantian}{are
+    available at the Quantian homepage}.
+  The interesting part for biologists is that Quantian contains in
+  addition all interesting packages of \DebianMed.  The author Dirk
+  Eddelbuettel, who is a Debian developer himself, just used the
+  simply to install biological software feature we provide and thus
+  made a great profit from \DebianMed.
+\item[Vigyaan - the biochemical software workbench]
+  \halfsloppy\printurl{www.vigyaancd.org}{Vigyaan} is an electronic
+  workbench for bioinformatics, computational biology and
+  computational chemistry.  It has been designed to meet the needs of
+  both beginners and experts.  VigyaanCD is a live Linux CD containing
+  all the required software to boot the computer with ready to use
+  modelling software.  VigyaanCD v0.1 is based on Knoppix v3.3.
+  Vigyann contains some programs which are not yet contained in
+  Debian.  It might be mutually beneficial to include these provided
+  that the license fits the DFSG.
+  \printurl{bioknoppix.hpcf.upr.edu}{BioKnoppix} is a customised
+  distribution of Knoppix Linux Live CD.  It is a very similar project
+  to the previous which specialises Knoppix for computational biology
+  and chemistry.
+\item[VLinux Bioinformatics Workbench]
+  Also \printurl{bioinformatics.org/vlinux}{VLinux} is at the time of
+  writing a Live CD based on the same outdated Knoppix version 3.3 as
+  Vigyann and includes a slightly changed software selection and
+  surely a different background layout.
+These are too many different initiatives that could all well do much more
+in order to share the burden of maintenance and updates. With Debian
+they have he right basic infrastructure. The time will show, whose packages
+will gain most momentum.
+\subsection{Bioinformatics and \DebianMed}
+\DebianMed is a Custom Debian Distribution with the aim to develop
+Debian into an operating system that is particularly well fit for the
+requirements for medical practice and research. The goal of \DebianMed
+is a complete system for all tasks in medical care which is build
+completely on free software.
+On the technical side \DebianMed contains a set of meta packages that
+declare dependencies on other Debian packages, and that way the
+complete system is prepared for solving particular tasks.  A special
+user menu will be created to enhance usability for the user working in
+the field of medicine.
+On the organisational side the project tries to attract people working
+in the field of Free Software in medicine to share the effort of
+building a common platform which reduces the amount of work for
+developers and users.  Sharing the effort in publishing free medical
+software to a large user base is a main advantage of \DebianMed.
+Currently inside \DebianMed applications are provided in certain
+categories: medical practice and patient management, medical research,
+hospital information systems, medical imaging, documentation,
+molecular biology and medical genetics and others.  The last part
+seems to be the most interesting and will be introduced in more detail.
+There are two so called meta packages which are named
+\package{med-bio} and \package{med-bio-dev}.  The sense of a meta
+package is that you have to install only one single package using a
+package management software inside Debian to get all interesting
+packages which are necessary for a single task.  For instance if a
+user types in: \\
+\hspace*{10mm}\texttt{apt-get install med-bio} \\
+all applications inside Debian which are related to the field of
+molecular biology and medical genetics will be installed.  Moreover
+system users will get an extra menu which contains all these
+applications.  The \package{med-bio-dev} package just installs
+programming libraries and tools which are interesting for users who
+want to develop biological applications (for instance the NCBI
+The strength of Debian is the huge number of developers (more than
+1000) all over the world working in different
+fields\ref{figure:weboftrust}.  Some of them are working in the field
+of biology or medicine and thus have a natural interest in developing
+a rock solid system they can relay on for their own work (not only
+commercial interest to sell service per accident).  That is the reason
+why Debian is often the platform of choice for researcher in the field
+of biology: They just find what their colleagues all over the world
+are using. The more the Debian user in the field of biology report
+back about problems or wishes the more Debian maintainers are able to
+enhance their system for their own and their users profit.
+%% Erwaehnung der wichtigsten Pakete, dann mit Referenzen
+Programming libraries:& \printurl{www.bioperl.org}{BioPerl},
+                        \printurl{www.biopython.org}{BioPython}\\
+Sequence similarity:  & \printurl{www.ncbi.nlm.nih.gov/BLAST}{BLAST2},
+                        \printurl{bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster}{Cluster3}$^*$,
+                        \printurl{www.ebi.ac.uk/clustalw}{ClustalW},
+                        \printurl{www.ncbi.nlm.nih.gov/sutils/e-pcr}{e-PCR}\\
+Pretty printing:      & \printurl{www.ch.embnet.org/software/BOX_form.html}{Boxshade},
+                        \printurl{homepages.uni-tuebingen.de/beitz/texshade.html}{TeXshade}$^*$,
+                        \printurl{homepages.uni-tuebingen.de/beitz/textopo.html}{Textopo}$^*$\\
+Phylogeny:            & \printurl{ftp.cse.sc.edu/bioinformatics/molphy}{Molphy},
+                        \printurl{evolution.genetics.washington.edu/phylip.html}{Phylip},
+                        \printurl{darwin.zoology.gla.ac.uk/~rpage/treeviewx}{Treeview} \\
+Tool collection:      & \printurl{www.emboss.org}{EMBOSS}$^{**}$,
+                        \printurl{emboss.sourceforge.net/apps/\#Embassy}{EMBASSY}$^{**}$,
+                        \printurl{www.bioconductor.org}{Bioconductor}$^*$, 
+                        \printurl{www.ncbi.nlm.nih.gov/Tools}{ncbi-tools library and programs},
+                        \printurl{www.arb-home.de}{ARB},
+                        \printurl{frodo.wi.mit.edu/primer3/primer3_code.html}{Primer3}$^*$\\
+Molecular modeling:   & \printurl{garlic.mefos.hr/garlic/index.html}{Garlic}\\
+Gene detection:       & \printurl{www.tigr.org/software/glimmer}{Glimmer},
+                        %GlimmerHMM$^*$,
+                        \printurl{www.sanger.ac.uk/Software/Artemis}{Artemis}$^{**}$\\
+Genetics:             & \printurl{www.biostat.jhsph.edu/~kbroman/qtl}{R/qtl}\\
+Viewers:              & \printurl{www.umass.edu/microbio/rasmol}{Rasmol},
+                        \printurl{www.hgmp.mrc.ac.uk/Registered/Option/treetool.html}{Treetool}\\
+Pattern discovery:    & \printurl{www-igm.univ-mlv.fr/~marsan/smile_english.html}{SMILE}$^*$,
+                        \printurl{hmmer.wustl.edu}{HMMer}\\
+\caption{Overview on packages in \DebianMed. $^*$ marks packages of collaborators of Debian Med that are not yet part of the Debian main distribution, $^{**}$ marks Debian packages made available through third parties.}\label{table:packages}
+Debian harbours the most known and well accepted tools in
+bioinformatics. An incomplete overview of these is given in table
+\ref{table:packages}. A more detailed overview is available at the
+  website}.  Debian has means to inform the community of programs that
+should be packed and the \DebianMed mailing list serves for an
+additional information transfer.
+Technically the Debian community has implemented functionalities for
+package management that have not been seen elsewhere. Originally
+motivated to achieve platform independence, all packages in the Debian
+Main distribution are required to be completely compilable and
+installable by a standardised set of commands. For all platforms,
+build daemons fully automated build binary packages upon the package
+maintainer's submission of a new source package.
+The \DebianMed project serves as a common platform for all Free
+Software that may be utilised in medical care. Tools developed in
+computational biology is just a part of it because it is an important
+brick in medical science.  With \DebianMed's
+ambition to become the platform of choice for biological work, conform
+with the principles of the
+  Policy}\cite{debianpolicy}, by the means of the distribution of
+development within the Debian Society, a well established reference
+platform for bioinformatics research and its medical applications has
+evolved and will continue to improve.  The organisation is open, both
+to new members and to external sites offering packages for
+From the perspective of data security it should be stressed that
+Debian GNU/Linux has the unique feature of the automated creation of
+\command{chroot} environments. In a dedicated directory, the minimal
+set of programs is stored to run a a Debian GNU/Linux system. A
+process started in such will not have file access to the remainder of
+the system with otherwise complete functionality.  The process is
+separated, even when started as root. Hence, arbitrary packages can be
+added and computations performed, be it for the build daemon or
+others, without accidentally or intentionally impeding the functioning
+of the underlying operating system.
+\subsection{Differences from other distributions}
+The Debian GNU/Linux distribution differs from others in several
+ways. Firstly, Debian is a non-commercial organisation of volunteers,
+that does not sell anything. The second and most appealing difference
+is the peer review and continuous pressure among the members to
+provide a high quality of packages. The Debian society has a constitution,
+elects its leader, and transparently describes policies for the
+creation of packages utilising specific technologies.
+With these principles, Debian achieved the largest collection
+of ready-to-install Free Software on the Internet.
+\subsubsection{Licensing issues}
+Several existing programs that might be useful for specialists are not
+free in the sense of the
+\printurl{www.debian.org/social\_contract\#guidelines}{Debian Free
+  Software Guidelines} \cite{dfsg}.
+Programs that are incompatible with the
+DFSG cannot be included in the Debian main distribution.
+One famous example of this group
+is \printurl{evolution.genetics.washington.edu/phylip.html}{PhyLip}
+and the same hold for ClustalW. Both programs' licenses contain a clause
+  Permission is granted to copy and use this program provided no fee
+  is charged for it and provided that this copyright notice is not
+  removed.
+As a consequence no reseller of Debian would be allowed to sell Debian
+because one CD contains PhyLip.
+Hence, this program may not be redistributed per default with the main
+and essential tools of Debian. Problems are, starting with those for the user:
+\item Need to obtain PhyLip from a different source
+\item If the user is not using a "common" architecture like {\ttfamily
+    i386} he might run into problems in compiling the latest version
+    as only the packages of the main distribution are submitted to the build daemons to save resources.
+%\item No extra security checks from his trusted operating system vendor.
+\item The user might not even notice that something like PhyLip exists
+  at all.  \DebianMed cares for pointing users to relevant software
+  and thus the user will be pointed to each single program package
+  {\itshape inside\/} Debian which of interest for biological
+  research.
+%While Debian Med supperts packages in the non-free section of
+%Debian this might be dropped at any time and has certain constraints.
+From the developers point of view we face also drawbacks:
+\item Possibly smaller user base (see last point above)
+\item Fewer bug reports and thus lower chance to increase the quality
+  of their software.
+\item \halfsloppy Porting problems to different architectures might
+  not be revealed early.
+While every author is perfectly free to choose this kind of license,
+Free Software experts agree that this kind of restrictions is
+possibly a drawback for those programs because they do not fully use
+the spinning power of Free Software development.
+\subsubsection{Importance of community support}
+That strong support within the community of users is essential for the
+development of software, for quality assurance, feedback on features,
+and not at least for the motivation of staff, all commercial
+distributors are well aware of.  E.g., RedHat has initiated Fedora as
+a free supplement to their commercial distribution.  It is this reason
+why \DebianMed is part of Debian and why groups external to the Debian
+society, like BioLinux, are also keen on close collaborations with the
+\subsubsection{Road map to come closer to \DebianMed}
+\item Join the \printurl{lists.debian.org/debian-med}{\DebianMed
+    mailing list}.
+\item Check what projects are missing and ask Debian maintainers for
+  official inclusion.  There is a sponsoring program by which even non
+  Debian developers can provide packages which are checked and
+  uploaded by official maintainers.  There is no point in keeping good
+  quality softwares outside of Debian.
+\item \halfsloppy Verify whether one needs special configuration for
+  your project.  If yes, verify which possibilities are given in the
+  Custom Debian Distribution effort.  It is more than collecting
+  software but bringing the software to your target users while taking
+  the burden from any configuration issues from his back.
+\item The only reason to keep things outside of Debian are licenses
+  which are not compatible with DFSG.  All other parts of your
+  projects can be included and your time for everyday package building
+  tasks can be saved and the workload shared with other people
+  following the same road.
+There are two ways to obtain Debian GNU/Linux:
+\item Installation from a CD that may be borrowed from a friend, or
+  bought from a commercial vendor. This may be together with a
+  computer magazine on a newsstand or from a redistributor on the
+  Internet.
+\item Download Debian from the web for free from a local mirror.
+The latter is the common way, a net install will only download the
+required packages.
+\subsubsection{Biological databases}
+The Debian community has yet not addressed the problem of
+incorporating biological databases into Debian. It seems not likely
+that this will happen in the Debian main distribution. The extra
+burden to maintain copies of e.g. the EMBL DNA sequence database on
+multiple mirrors of Debian puts too much of a burden to the mirrors
+with only little gain.  And not everybody requires regular updates
+with the associated network traffic and the induced instability when
+exchanging the files while scripts might still be running reading the
+data.  The provision of a set of tools that provides updates on demand
+seems a more likely scenario.  This would then also need to manage the
+update of indices of e.g. sequence similarity tools.
+For now, Debian offers libraries like BioPerl with its facility to
+access online repositories, circumventing problems with the updating
+of local data.  Debian is well suited though to address the issue
+because of its means of introspection, the programmer can tell which
+databases are installed and what files are available.
+We have shown that there is a considerable heterogeneous shape of Free
+Software in biology. The continuous updates of data and the addition of
+novel important tools for a general bioinformatics environment cannot
+be performed by a single maintainer. The adherence to a policy and the
+sharing of maintenance are basic technologies to allow
+inter-institutional software projects of different kind in health care.
+Debian and its special dedication to software in computational biology
+in \DebianMed, but also the technical infrastructure behind this
+community project renders a comfortable solution.  The volunteers
+behind \DebianMed strive to support everybody's specific projects as
+best as they possibly can. It is the particular challenge of users of
+Free Software, to determine together with the community the available
+packages that already serve their needs or may be adapted
+For Debian GNU/Linux to become the race-horse for Free Software in
+health care, further important software which is listed at
+  list of open source healthcare software}\cite{wikipediaoslist:2008}
+like for instance OpenVista\cite{openvista:2008} and other enterprise
+grade health care information systems has to be packaged for Debian.
+Whatever choice for an infrastructure is made, with Debian it is available
+to all collaborating sites almost instantly.
+The authors thank the Debian Developers for all their work and
+particularly those who have contributed to \DebianMed and the Debian
+Pure Blends effort which builds a common framework around similar
+projects like Debian Edu for education, Debian Science for scientific
+work and others. Debian is supported by donations through
+\printurl{www.spi-inc.org}{Software in the Public Interest}, a
+non-profit umbrella organisation for free software projects.

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