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} _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
