[med-svn] r3288 - trunk/community/talks/200906_bosc

Mon Apr 13 21:28:59 UTC 2009

Author: smoe-guest
Date: 2009-04-13 21:28:58 +0000 (Mon, 13 Apr 2009)
New Revision: 3288

Modified:
   trunk/community/talks/200906_bosc/abstract.tex
Log:
Abstract for BOSC as it was just submitted.


Modified: trunk/community/talks/200906_bosc/abstract.tex
===================================================================

--- trunk/community/talks/200906_bosc/abstract.tex	2009-04-13 16:56:28 UTC (rev 3287)
+++ trunk/community/talks/200906_bosc/abstract.tex	2009-04-13 21:28:58 UTC (rev 3288)
@@ -1,29 +1,41 @@
 % Abstract for http://open-bio.org/wiki/BOSC_2009
 
 \documentclass[10pt,smallheadings]{scrartcl}
+\pagestyle{empty}
 \usepackage{geometry}
 \usepackage{hyperref}
-\geometry{a4paper,left=30mm,right=30mm, top=2.5cm, bottom=2.5cm} 
+\geometry{a4paper,left=30mm,right=30mm, top=2.5cm, bottom=2cm} 
 \usepackage[utf8x]{inputenc}
-\title{Debian adopts and disseminates Bioinformatics Open Source Software}
-\author{Steffen Möller \and Charles Plessy \and David Paleino \and Andreas Tille}
-\date{Debian Community}
+%\title{Debian adopts and disseminates Bioinformatics Open Source Software}
+%\author{Steffen Möller \and Charles Plessy \and David Paleino \and Andreas Tille}
+%\date{Debian Community}
 \begin{document}
-\maketitle
+%\maketitle
+\begin{centering}
+{\bf \large Debian adopts and disseminates Bioinformatics Open Source Software}
+
+{\small
+Steffen Möller, Charles Plessy, David Paleino, Andreas Tille and the Debian Community$^*$
+}
+
+\end{centering}
+
 \section*{Looking back}
 
-In Bioinformatics we are used to associate technological advantage with
-the advacements in wet-lab techniques that bring us a steadily increased 
+In Bioinformatics we are used to associate technological progress with
+the advancements in wet-lab techniques that bring us a steadily increased 
 influx of more and more novel data to manage and interpret. Over that
-we often forget, that this is only possible since the IT sciences have
-evolved even quicker. This allows us to keeping pace with the data stream while
-have more
-analyses being applied and to even tap into the combinatorial integration
-of the wet-lab findings and its presentation back to biological researchers.
+we often forget that this is only possible since the IT sciences have
+evolved even more quickly. This allows us to keeping pace with the data stream while
+applying even more
+analyses.
+% for full paper
+%, to even tap into the combinatorial integration
+%of the wet-lab findings and to present the findings back to biological researchers.
 
-When the first Bioinformatics Open Source Conferences (BOSC) were held in the late 90s,
+When the first Bioinformatics Open Source Conferences were held in the late 90s,
 the Internet was still a recent event. To find data on the net was considered
-special. And that data came at no extra charge. GNU/Linux emerged as the ubiquitous
+special. And that data came at no extra charge. GNU/Linux had emerged as the ubiquitous
 operating system, as free as the data that was analysed with it. And free were
 most tools for sequence analysis, with development often funded by the same
 institutions that funded the wet-lab production of the data. Free also became
@@ -31,10 +43,10 @@
 
 These libraries and many accompanying tools are now being used in many
 different suites for the handling of biological data. Or they are being
-used for smallish scripts to help with analyses in smaller or larger
+used by smallish scripts to help with analyses in smaller or larger
 research projects. They became a commodity. One has gained sufficient
 confidence in the community to always want the latest versions of these
-helpers. Many take the existence of these tools for granted. Again others
+helpers. Many analysts take the existence of these tools for granted or
 use them as part of a larger tool while not being aware of them. And those
 distributing software that is depending on common libraries or tools need
 ways to ensure a trustworthy installation of the basic research infrastructure.
@@ -43,47 +55,50 @@
 
 \section*{Today}
 
-GNU/Linux distributions live from their users. Commercial distributions (Novel, RedHat)
-have all opened up for packages organised by the community (OpenSuSE, Fedora),
-and Debian GNU/Linux has been a Community-driven distribution ever since. And it
-is that distribution which ships the largest number of bioinformatics packages
-for the largest number of platforms.
+GNU/Linux distributions live from their users. Commercial distributions
+have opened up for packages organised by the community, i.e. via OpenSuSE and Fedora.
+Debian GNU/Linux has been a community-driven distribution ever since and with
+around 50 programs or libraries (plus dependencies) it is the distribution
+which ships the largest number of bioinformatics packages for the largest
+number of platforms.
 
-Since 2001, Debian has come up with the concept of Debian Custom Distributions,
-which are now called Debian Blends, which is
+In 2001 Debian introduced a concept now called Debian Blends, 
 a platform for the presentation of software packages for communities with
 a distinct interest. Bioinformatics is well kept under the hood of the
 Debian-Med blend with some packages also being found under Debian-SciComp
 or Debian-Science.
-
 Individuals interested to see a bioinformatics software packaged will send
 an email to the mailing list or fill out a Request for Packaging. Quite
 often it is a Debian packager amongst the developers of the software or
 an enthusiastic user, who seeks his self-prepared package to be shipped
 with the distribution.
 
-Many packages are community-maintained such that work to update packages
-is shared amongst many. The package descriptions are translated to many
-languages, which along will be beyond a single individual's skill set
-and helps in promoting the software.
+% For the full paper
+%Many packages are community-maintained such that work to update packages
+%is shared amongst many. The package descriptions are translated to many
+%languages, which along will be beyond a single individual's skill set
+%and helps in promoting the software.
 
 \section*{Looking forward}
 
-Debian is strong in providing a coherent installation of an enormous
-wealth of software.  It directly reflects the progress that the Open
-Source community is experiencing.
+% For full paper
+%Debian is strong in providing a coherent installation of an enormous
+%wealth of software.  It directly reflects the progress that the Open
+%Source community is experiencing.
 
-A major problem of bioinformatics is the local maintenance of remotely
+A major problem in bioinformatics is the local maintenance of remotely
 accessibly data.  Every group performing research in this field is solving
 this to their local needs in some way, crafting a series of scripts,
-but this effort should somehow be shared. This topic is addressed in a
-Google Summer of Code project, the outcome of which will be interesting
-to evaluate.
+but this effort should somehow be shared.
+% For full paper
+%This topic is addressed in a
+%Google Summer of Code project, the outcome of which will be interesting
+%to evaluate.
 
 Where Debian, like all other Linux distributions, need help, and this also
 is particularly obvious in the complex interplay of software in
 Bioinformatics, is the guidance of users in the interplay of multiple
-tools. There is no package for the education of users or for pre-assembled
+tools. There is yet no package for the education of users or for pre-assembled
 workflows that address frequently observed problems. This issues was raised
 in past discussions in the context of the possibility to prepare a BOSC
 liveCD, which may also be imaginable as an interplay of a regular Linux
@@ -91,6 +106,11 @@
 
 \section*{Availability}
 
-The Debian home page is \url{http://www.debian.org}, development on Bioinformatics packages is best monitored on \url{http://debian-med.alioth.debian.org}.
+The Debian home page is \url{http://www.debian.org}, development on
+bioinformatics packages is best monitored on \url{http://debian-med.alioth.debian.org}.\\
 
+{\small
+$^*$ to whom correspondence should be addressed: debian-med at lists.debian.org
+}
+
 \end{document}


