[Cdd-commits] r1170 - projects/med/trunk/papers/09_osehc_porto

CDD Subversion Commit noreply at alioth.debian.org
Thu Oct 30 15:48:15 UTC 2008 

Author: tille
Date: Thu Oct 30 15:48:15 2008
New Revision: 1170

Added:
   projects/med/trunk/papers/09_osehc_porto/authorstat.pdf
   projects/med/trunk/papers/09_osehc_porto/dmstats.pdf
Modified:
   projects/med/trunk/papers/09_osehc_porto/debian-med-bio.tex
   projects/med/trunk/papers/09_osehc_porto/paper-text.tex
Log:
Results


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Modified: projects/med/trunk/papers/09_osehc_porto/debian-med-bio.tex
==============================================================================
--- projects/med/trunk/papers/09_osehc_porto/debian-med-bio.tex	(original)
+++ projects/med/trunk/papers/09_osehc_porto/debian-med-bio.tex	Thu Oct 30 15:48:15 2008
@@ -54,10 +54,10 @@
    \xspace
 }
 
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Added: projects/med/trunk/papers/09_osehc_porto/dmstats.pdf
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Modified: projects/med/trunk/papers/09_osehc_porto/paper-text.tex
==============================================================================
--- projects/med/trunk/papers/09_osehc_porto/paper-text.tex	(original)
+++ projects/med/trunk/papers/09_osehc_porto/paper-text.tex	Thu Oct 30 15:48:15 2008
@@ -160,7 +160,7 @@
 
 \begin{figure*}
 \centering
-\myinsertgraphic{earthkeyring}
+\myinsertgraphic{earthkeyring}{80mm}{53mm}
 \caption{Debian web of trust}\label{figure:weboftrust}
 \end{figure*}
 
@@ -433,6 +433,8 @@
 
 \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
@@ -448,21 +450,22 @@
 care as well.  This goal is not yet reached but continuous work is
 done into this direction and some important steps are done.
 
-An even more important difference than the more general approach of
-\DebianMed is the fact that \DebianMed is not only about just
-packaging software.
-
-\DebianMed is a Debian Pure Blend 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
+\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.
 
-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.
+\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
@@ -470,80 +473,80 @@
 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.  The last part
-seems to be the most interesting and will be introduced in more detail.
+molecular biology and medical genetics and others.
 
-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
+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.  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
+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}).
 
-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}\\
-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}\\
-\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
-additional information transfer.
+
+\subsubsection{Continuous growth}
+
+\begin{figure*}
+\centering
+\myinsertgraphic{dmstats.pdf}{120mm}{80mm}
+\caption{Number of dependencies of selected metapackages}\label{figure:dmstats}
+\end{figure*}
+
+\begin{figure*}
+\centering
+\myinsertgraphic{authorstat.pdf}{120mm}{80mm}
+\caption{Activity of most active authors on the \DebianMed mailing list}\label{figure:authorstats}
+\end{figure*}
+
 
 \section{Discussion}

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