[med-svn] r3286 - in trunk/community/talks: . 200906_bosc

[Andreas Tille]

Author: tille
Date: 2009-04-12 21:42:13 +0000 (Sun, 12 Apr 2009)
New Revision: 3286

Added:
   trunk/community/talks/200906_bosc/
   trunk/community/talks/200906_bosc/abstract.tex
Log:
Abstract for BOSC


Added: trunk/community/talks/200906_bosc/abstract.tex
===================================================================
--- trunk/community/talks/200906_bosc/abstract.tex	                        (rev 0)
+++ trunk/community/talks/200906_bosc/abstract.tex	2009-04-12 21:42:13 UTC (rev 3286)
@@ -0,0 +1,95 @@
+% Abstract for http://open-bio.org/wiki/BOSC_2009
+
+\documentclass[10pt,smallheadings]{scrartcl}
+\usepackage{geometry}
+\usepackage{hyperref}
+\geometry{a4paper,left=30mm,right=30mm, top=2.5cm, bottom=2.5cm} 
+\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}
+\begin{document}
+\maketitle
+\section*{Looking back}
+
+In Bioinformatics we are used to associate technological advantage with
+the advacements with 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, by keeping pace with the data stream with more
+analyses being applied and even tapping into the combinatorial integration
+of the wet-lab findings and its presentation back to biological researchers.
+
+When the first Bioinformatics Open Source Conferences (BOSC) 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
+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
+the Bio\{Perl,Java,*\} libraries that help analysing the sequence data.
+
+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
+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
+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.
+They can give instructions to their users to install everything themselves,
+can ship precompiled binaries or -- suggest a GNU/Linux distribution's packages.
+
+\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.
+
+Since 2001, Debian has come up with the concept of Debian Custom Distributions,
+which are now called Debian Blends, which is
+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.
+
+\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.
+
+A major problem of 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.
+
+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
+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
+distribution with a set of Wiki pages to guide the users. 
+
+\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}.
+
+\end{document}