# [med-svn] r5531 - in trunk/community/papers: . 09_osehc_porto

Andreas Tille tille at alioth.debian.org
Fri Dec 3 09:42:53 UTC 2010

Author: tille
Date: 2010-12-03 09:42:53 +0000 (Fri, 03 Dec 2010)
New Revision: 5531

trunk/community/papers/09_osehc_porto/
trunk/community/papers/09_osehc_porto/Makefile
trunk/community/papers/09_osehc_porto/authorstat.pdf
trunk/community/papers/09_osehc_porto/debian-med-bio.bib
trunk/community/papers/09_osehc_porto/debian-med-bio.tex
trunk/community/papers/09_osehc_porto/dmstats.pdf
trunk/community/papers/09_osehc_porto/earthkeyring.png
trunk/community/papers/09_osehc_porto/narrow.sty
trunk/community/papers/09_osehc_porto/paper-text.tex
trunk/community/papers/09_osehc_porto/paper-text_longversion.tex
Log:
Moved paper from Blends to Debian Med SVN

===================================================================
--- trunk/community/papers/09_osehc_porto/Makefile	                        (rev 0)
+++ trunk/community/papers/09_osehc_porto/Makefile	2010-12-03 09:42:53 UTC (rev 5531)
@@ -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 20000 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}
+\item[tasksel] 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 Blend 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[command line package management] \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.
+
+\item[GUI] There are several graphical user interfaces to manipulate
+  the installation of packages on a Debian installation.  The most
+  popular is currently \command{synaptic} which eneables users to seek
+  for certain packages and displays detailed information about each
+  package.
+\end{description}
+
+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{Comparable 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, policy compliant Debian packages
+  because they install files into \Path{/usr/local} hierarchy in
+  contrast to the Debian policy which does not allow files inside
+  packages at this location because \Path{/usr/local} is reserved for
+  locally installed files that do not fall under responsibility of the
+  Debian package manager.
+
+  Besides this technical fact Bio-Linux authors were not that strict
+  regarding licensing and copyright of packaged projects.  Every
+  official Debian package has to comply to the Debian Free Software
+  Guidelines DFSG and the copyright information has to be shipped with
+  the source of a binary Debian package has to be provided next to the
+  binary.  All these very important requirements are not fulfilled in
+  most cases in Bio-Linux.
+
+  However, the authors did a great job in collecting a certain amount
+  of very useful software for biologists and the \DebianMed project
+  is seeking for possibilities for cooperation.
+
+\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.
+
+\end{description}
+
+\subsection{Other repositories of biology related software}
+
+Looking beyond Debian and related distributions which share more or
+less the same technique we find similar efforts to deliver sets of
+
+\begin{description}
+
+\item[FreeBSD Ports: Biology] The Free Software world does not only
+  know Linux as free operating system.  There are others out there
+  like several BSD derivates, OpenSolaris, Hurd and others.  The
+  FreeBSD project has a really nice
+  \printurl{http://www.freebsd.org/ports/biology.html}{collection of
+    biological software}.
+\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{Comparison with \DebianMed}
+
+\subsubsection{Other fields than only biology}
+
+Looking at all the projects above it becomes evident that they are all
+dealing only with biological software.  Above it was stated that one
+strong column of \DebianMed is this specific field and it is for a
+reason:  The amount of free biological software is large and most of
+these projects are relatively easy to turn into packages - so the
+amount of work per package is much smaller compared to for instance
+medical record applications with preparation of databases, dedicated
+user management, etc.
+
+So there is one major difference between the projects mentioned above
+and \DebianMed: While the biological part is really interesting for
+medical care \DebianMed tries to cover all other fields of medical
+care as well.  This goal is not yet reached but continuous work is
+done into this direction and some important steps are done.
+
+\subsubsection{Debian Pure Blend}
+
+An even more important difference than the more general approach
+compared to the other repositories is the fact that \DebianMed is not
+only about just packaging software.  The \DebianMed project is one of
+the earliest so called {\em Debian Pure Blends} (formerly known as
+Custom Debian Distributions) and just wants to do more for the comfort
+of their users than adding binary packages to the Debian package pool.
+The main goal is to turn Debian into the distribution of choice for
+people working in the field of medicine and to make Debian 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.
+
+
+\subsubsection{Flexibility in supporting small user groups}
+
+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.
+
+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).  So sometimes the
+chances to realise specific support for small user groups are better
+inside a community driven distribution than in a commercial
+distribution: You just need some developers who have a specific
+interest and they will realise and publish an environment for their
+needs and will share it with other users.  A company that has to gain
+a certain market share is not flexible enough in this regard to cover
+very specific interests.
+
+The underlying principle that those things will be done if there is
+somebody who just does the work is called {\em Do-O-Cracy} -- which
+just means the doer decides what gets done.
+
+That is the reason why Debian is often the platform of choice for
+researcher in the field of biology: Some biologists are Debian
+maintainers and so they added support for biological packages. 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.
+
+\subsubsection{Metapackages}
+
+On the technical side \DebianMed contains a set of metapackages that
+declare dependencies on other Debian packages, and that way the
+complete system is prepared for solving particular tasks.  So the user
+has not to deal with the large number of package descriptions of 20000
+packages inside the Debian distribution -- it is just enough to seek
+for metapackages starting with prefix \package{med-} and install the
+metapackage of choice.  The package management system will care for
+the installation of all packages that are in the list of dependencies
+of this metapackage - so the user can be sure that all packages he
+might need for the job will be installed on his system.  Once one of
+the metapackages is installed a special user menu will be created to
+enhance usability for the user working in the field of medicine.
+
+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.
+
+There are two so called metapackages 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.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}).
+
+
+\subsubsection{Continuous growth}
+
+Several Free Software projects which try to deal with small user group
+software started with a lot of enthusiasm but at some point in time
+developers had other interests or just were unable to maintain the
+project because of lack of man power.  The strategy of \DebianMed is
+to stay strictly inside Debian -- so even if manpower is a problem the
+whole infrastructure around will stay solid and does not drain extra
+resources.  So nobody of the \DebianMed team has to care about writing
+installers, running an online repository and mirrors work on a bug
+tracking system etc.  All this infrastructure is just there.
+
+\begin{figure*}
+\centering
+\myinsertgraphic{dmstats.pdf}{120mm}{80mm}
+\caption{Number of dependencies of selected metapackages}\label{figure:dmstats}
+\end{figure*}
+
+The success of this strategy can be proven by a continuous growth for
+instance if the number of packages inside Debian which is interesting
+for health care.  Taking the number of dependencies of some
+metapackages into account (see figure \ref{figure:dmstats}) at the
+beginning of the project in 2002 a quite low number of packages useful
+for medical care was available.  A nearly linear growth with a
+gradient that perfectly reflects the availability of programs in this
+field can be observed.
+
+\begin{figure*}
+\centering
+\myinsertgraphic{authorstat.pdf}{120mm}{80mm}
+\caption{Activity of most active authors on the \DebianMed mailing list}\label{figure:authorstats}
+\end{figure*}
+
+\enlargethispage{10mm}
+This growth of the output of a project is an important part but
+we also try to measure the commitment of the people involved in the
+project.  It has to be ensured that fresh blood is flooding into the
+project to make sure it can cope with the normal loss of supporters
+which always happens in Free Software projects (people find new jobs
+with different orientation or less spare time for private reasons
+etc.)  A raw measure for the activity of members might be their mails
+to the project mailing list.  Figure \ref{figure:authorstats}) shows
+the number of mails of the ten most active posters of the \DebianMed
+mailing list.  This graph shows perfectly that the number of active
+supporters is growing solidly.  In the last two years three people can
+be considered as very active and there is no dramatic loss of people
+in the project.  The general activity on the mailing list is
+constantly growing.
+
+
+\subsubsection{Role inside Debian}
+
+The Debian Pure Blends framework was mainly inspired by the \DebianMed
+needs.  Regarding implementation the Debian Edu project -- another
+Blend -- is much more advanced.  There are several reasons for this
+fact.  The main reasons are the availability of software for education
+and the fact that a Norwegian company payed developers to work full
+day on this project.  \DebianMed tried to gain profit from common
+technologies and generalised some tools of Debian Edu for all Blends.
+Moreover inside \DebianMed some new Blend tools were developed which
+enhance the easy build of metapackages.  The latest contribution to
+the Blend framework is a set of automatically generated web pages
+which can be used by any Blend.  For instance there is an overview
+practice management) which provides a nice list of all the packages
+including some metainformation and the description of the packages in
+this task.  So the output of the project can be easily viewed at
+  of \DebianMed}.
+
+By providing this kind of tools for other Blends as well \DebianMed
+has set some cornerstone in the technical cooperation between user
+oriented projects inside Debian.  This in turn awakes the interest of
+other Debian developers who might provide other tools for \DebianMed.
+
+\section{Discussion}
+
+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 medical 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.
+
+
+\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 supports 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.
+  page of \DebianMed} mentioned above does not only contain the work
+  that was done -- it contains also a nicely formated list which
+  projects would be interesting to reach the final goal to cover each
+  task in medical care with Free Software.  This list inside each
+  section might give some idea where help might be needede.
+\item \halfsloppy Verify whether one needs special configuration for
+  your project.  If yes, verify which possibilities are given in the
+  Debian Pure Blends 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}
+
+
+\section{Conclusions}
+
+We have shown that there is a considerable heterogeneous shape of Free
+Software for medical care even if some fields like micro biology are
+better covered than others. The continuous updates of data and the
+addition of novel important tools for a general medical 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 medical software 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 author thanks 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