[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/
projects/med/trunk/papers/09_osehc_porto/Makefile
projects/med/trunk/papers/09_osehc_porto/debian-med-bio.bib
projects/med/trunk/papers/09_osehc_porto/debian-med-bio.tex
projects/med/trunk/papers/09_osehc_porto/earthkeyring.png   (contents, props changed)
projects/med/trunk/papers/09_osehc_porto/paper-text.tex
Log:
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.

==============================================================================
--- (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
+
+text=debian-med-bio
+
+DISTDIR=debian-bio-0.2
+
+%.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/" \
+	    $(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 $(DISTDIR) debian-med-bio + +clean: + rm -f$(text)*.log $(text)*.aux$(text)*.dvi $(text)*.toc$(text)*.out $(text)*.bbl$(text)*.blg
+	rm -f *.log
+	rm -f earthkeyring.eps
+
+dist:
+	mkdir -p $(DISTDIR)/paper + cp -a *.tex *.css Makefile$(DISTDIR)/paper
+	tar -czf $(DISTDIR).tgz$(DISTDIR)
+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:
+\begin{description}
+  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.
+\end{description}
+
+
+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
+(\printurl{fink.sourceforge.net}{fink.sourceforge.net}).
+
+
+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
+be:
+\begin{itemize}
+  \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.
+\end{itemize}
+
+The best established Distributors of GNU/Linux systems are
+\printurl{www.mandrakelinux.com}{Mandrake},
+\printurl{www.redhat.com}{RedHat}, \printurl{www.suse.com}{SuSE} (now
+owned by \printurl{www.novell.com/linux}{Novell}) and
+\printurl{www.debian.org}{Debian}.
+\printurl{www.linspire.com}{Linspire},
+\printurl{www.xandros.com}{Xandros},
+\printurl{www.mepis.org}{MEPIS} and
+\printurl{www.ubuntulinux.org}{Ubuntu} are well known derivates of
+Debian.
+
+\section{Results}
+
+\subsection{Bioinformatics and Debian-associated repositories}
+
+
+\begin{description}
+
+\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
+  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
+    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{forester}, etc.  You will {\em also need to edit} the
+    \Path{aliasrc} file to reflect the location of the Java binaries
+  \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.
+
+\item[bioinformatics.debian.net]
+
+  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.
+
+\end{description}
+
+
+\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
+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}.
+
+
+\begin{description}
+\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
+  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.
+
+\item[BioKnoppix]
+
+
+  \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.
+
+\end{description}
+
+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
+library\cite{Wheeler2005,Jenuth2000,ncbi:2004}).
+
+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
+\begin{table}
+\begin{tabular}{rp{48mm}}
+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}\\
+                        \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}\\
+\end{tabular}
+\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}
+\end{table}
+
+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
+\printurl{www.debian.org/devel/debian-med/microbio}{\DebianMed
+  website}.  Debian has means to inform the community of programs that
+should be packed and the \DebianMed mailing list serves for an
+
+\section{Discussion}
+
+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
+\printurl{www.debian.org/doc/debian-policy}{Debian
+  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
+installations.
+
+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
+like
+\begin{quote}
+  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.
+\end{quote}
+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:
+\begin{itemize}
+\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.
+\end{itemize}
+
+%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:
+\begin{itemize}
+\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.
+\end{itemize}
+
+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
+community.
+
+
+\subsubsection{Road map to come closer to \DebianMed}
+
+\begin{enumerate}
+\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
+\end{enumerate}
+
+There are two ways to obtain Debian GNU/Linux:
+\begin{enumerate}
+\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.
+\end{enumerate}
+
+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 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.
+
+
+\section{Conclusions}
+
+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
+respectively.
+
+health care, further important software which is listed at
+\printurl{http://en.wikipedia.org/wiki/List_of_open_source_healthcare_software}{Wikipedia
+  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.
+
+\subsection*{Acknowledgements}
+
+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