[med-svn] r1287 - in trunk/community: . papers papers/debianMedBio

[smoe-guest at alioth.debian.org]

Author: smoe-guest
Date: 2008-02-03 23:20:26 +0000 (Sun, 03 Feb 2008)
New Revision: 1287

Added:
   trunk/community/papers/
   trunk/community/papers/debianMedBio/
   trunk/community/papers/debianMedBio/Makefile
   trunk/community/papers/debianMedBio/paper.bib
   trunk/community/papers/debianMedBio/paper.tex
Log:
Dumping thoughts about what could be in a paper that is describing Debian to the community of computational biologists. Feel free to join in.



Added: trunk/community/papers/debianMedBio/Makefile
===================================================================
--- trunk/community/papers/debianMedBio/Makefile	                        (rev 0)
+++ trunk/community/papers/debianMedBio/Makefile	2008-02-03 23:20:26 UTC (rev 1287)
@@ -0,0 +1,12 @@
+all: paper.pdf
+
+paper.pdf: paper.tex
+	pdflatex paper
+	bibtex pdflatex
+	pdflatex paper
+
+
+look: paper.pdf
+	kpdf paper.pdf
+
+.PHONY: look all

Added: trunk/community/papers/debianMedBio/paper.bib
===================================================================

Added: trunk/community/papers/debianMedBio/paper.tex
===================================================================
--- trunk/community/papers/debianMedBio/paper.tex	                        (rev 0)
+++ trunk/community/papers/debianMedBio/paper.tex	2008-02-03 23:20:26 UTC (rev 1287)
@@ -0,0 +1,86 @@
+\documentclass{article}
+\author{Debian-Med package maintainers}
+\title{Debian Linux for Desktops and Compute Clusters in Computational Biology}
+\date{}
+\begin{document}
+\maketitle
+\begin{abstract}
+\section{Availability:} http://www.debian.org
+\section{Contact:} debian-med at lists.debian.org
+\end{abstract}
+
+\section{Introduction}
+
+An enormous amount of computer programs have been developed to support
+the handling and the analysis of data in biological research. In fact,
+in many scientific disciplines, here biological sequence analysis or
+structural biology, the interpretation of data presented by computers
+became intrinsic to biological research. Groups develop tools and make
+them public, allowing others to confirm their findings, learn and further
+develop these techniques.
+
+The last years brought a better understanding of the interaction of the
+molecules. The modelling of biological processes thus also brought an
+increased intertwining computational tools.  This led to the development
+of workflow tools and advent of grid computing.  In larger research
+groups, system administrators experience the difficulty to keep these
+many programs updated. Smaller groups or those with an emphasis on
+the wet lab will leave this burden on the individual researchers. The
+situation is aggravated by the challenge to synchronise installations
+across collaborating sites.
+
+A major operating system in computational biology is Linux. Here, the
+distribution of software is organised in packages. For more than 10 years,
+the volunteer-run Debian Linux distribution helps organising the community
+to share the burden of package management. And it embraces researchers like
+computational biologists to join in for everyone's benefit. This paper
+outlines the achievements of the Debian Linux community to provide a free
+infrastructure for computational biology.
+
+\section{Approach}
+
+\subsection{Organisation}
+
+Debian redistributes software as source packages or as precompiled
+binaries for 11 different platforms. The prior come with build
+instructions which can be executed automatically. All platforms are equal in
+their file system structure.
+
+A prime condition for the inclusion of software with Debian is the
+compatibility with the Debian Free Software Guidelines, which in complete
+harmony with scientific principles demands the software to be rebuildable
+and redistributable. The Debian packager adds additional value to the
+original distribution by adding man pages for each binary and providing
+menu items for the user's desktop.
+
+\subsection{DebTags}
+
+% can we summarise how the DebTags work 
+
+\section{Results}
+
+% our packages should be listed here
+
+\section{Discussion}
+
+Debian together with all these distributions that its core infrastructure
+and allow the installation of Debian packages (Ubuntu, Skolinux,
+...) are of considerable help for scientists at all stages of their
+education. These packages are commonly maintained by researchers in
+the field. Often these also come with data for testing or with complete
+tutorials. This also allows interested laymen to investigate these tools
+and the scientific problems these address - around the globe.
+
+\section*{Acknowledgements}
+
+The authors in the name of all Debian package maintainers thank all the developers of the software that is made available. Thanks also goes to the users who helped to further improve our infrastructure for science.
+% Is that too pathetic?
+
+\section*{Authors}
+
+Steffen M\"oller, University of L\"ubeck, Germany
+and everyone on Debian-Med / Debichem shall be invited to join for this publication.
+
+\bibliographystyle{PLoS-Biology}
+\bibliography{paper}
+\end{document}