[med-svn] r5543 - trunk/community/papers/11_med-floss_luxemburg

Tue Dec 7 22:52:08 UTC 2010

Author: tille
Date: 2010-12-07 22:52:08 +0000 (Tue, 07 Dec 2010)
New Revision: 5543

Modified:
   trunk/community/papers/11_med-floss_luxemburg/paper-text.tex
Log:
Drop paragraphs about dead live CDs


Modified: trunk/community/papers/11_med-floss_luxemburg/paper-text.tex
===================================================================

--- trunk/community/papers/11_med-floss_luxemburg/paper-text.tex	2010-12-06 23:14:16 UTC (rev 5542)
+++ trunk/community/papers/11_med-floss_luxemburg/paper-text.tex	2010-12-07 22:52:08 UTC (rev 5543)
@@ -1,20 +1,20 @@
 \newcommand{\DebianMed}{Debian\ Med\xspace}
 
 \begin{abstract}
-  The Debian Med project started in 2002 with the objective to bring
+  The \DebianMed project started in 2002 with the objective to bring
   free medical software into the focus of users. The first step was
   the investigation of available Free Software in this area and to
   accomplish the conditions for a simple and solid installation of
-  this software in Debian GNU/Linux.  It has shown that the Debian Med
+  this software in Debian GNU/Linux.  It has shown that the \DebianMed
   project has a positive effect for the cooperating upstream projects.
 
   The fields molecular biology and medical imaging were covered quite
   good with Free Software solutions and there are even Free Software
-  projects to manage a medical practice. The Debian Med project tries
+  projects to manage a medical practice. The \DebianMed project tries
   to be the missing link between developers and users to support Free
   Software solutions for all areas in medicine.
 
-  Debian Med is intended to be useful for service providers who want
+  \DebianMed is intended to be useful for service providers who want
   to distribute their free or proprietary solutions in medical care.
 
   The whole project is embeded into the Debian Pure Blends framework
@@ -279,56 +279,6 @@
 
 \section{Results}
 
-\subsection{Comparable Debian-associated repositories}
-
-\begin{description*}
-
-\item[Bio-Linux Bioinformatics package repository]
-
-  \halfsloppy The Bio-Linux Bioinformatics package repository contains
-  the \printurl{envgen.nox.ac.uk/pkg\_repository.html}{Bio-Linux 4
-    bioinformatics software} and can be installed from a centralised
-  repository located on the EGTDC server.  The packages available from
-  this site have been created by the EGTDC specifically for the
-  Bio-Linux project and are in deb format.
-
-  The packages are not, however, policy compliant Debian packages
-  because they install files into \Path{/usr/local} hierarchy in
-  contrast to the Debian policy which does not allow files inside
-  packages at this location because \Path{/usr/local} is reserved for
-  locally installed files that do not fall under responsibility of the
-  Debian package manager.
-
-  Besides this technical fact Bio-Linux authors were not that strict
-  regarding licensing and copyright of packaged projects.  Every
-  official Debian package has to comply to the Debian Free Software
-  Guidelines (DFSG) and the copyright information has to be shipped
-  with the file \Path{/usr/share/doc/<packagename>/copyright}.
-  Moreover the source of a binary Debian package has to be provided
-  next to the binary.  All these very important requirements are not
-  fulfilled in most cases in Bio-Linux.
-
-  However, the authors did a great job in collecting a certain amount
-  of very useful software for biologists and the \DebianMed project
-  is seeking for possibilities for cooperation.
-
-\item[BioLinux-BR Project]
-
-  \halfsloppy A similar project is the
-  \printurl{biolinux.df.ibilce.unesp.br/index.en.php}{BioLinux-BR
-    Project} which is a project directed to the scientific community.
-  Their goal is to create a Linux distribution for people with little
-  familiarity with the installation of the operational system and
-  mainly for people who do not know to proceed unpacking a program,
-  compile and install it correctly.
-
-  In fact, this project has assembled a huge amount of packages,
-  probably the most complete collection of Free Software in biology.
-  Packages for multiple distributions are provided, which includes
-  Debian, and a live CD.
-
-\end{description*}
-
 \subsection{Other repositories of biology related software}
 
 Looking beyond Debian and related distributions which share more or
@@ -347,62 +297,6 @@
 
 \subsection{Dedicated bioinformatics and medical distributions}
 
-\ifmetacomment
-The concept of a live CD allows to create a CD or DVD that boots a
-computer, starts a defined set of application without a user's
-intervention and has all tools in place that suits a particular
-community.  Such provide fully featured Linux workstations without
-additional installations of access to local disk space, alternatively
-booting via the network is supported by Debian, which particularly
-appeals to Blades or large clusters. The most successful such LiveCD
-is the Debian-derived Knoppix\cite{knopper:2005}.
-
-\begin{description*}
-\item[The Quantian Scientific Computing Environment]
-
-  Quantian is a remastering of a well established effort
-  (\printurl{www.knopper.net/knoppix/index-en.html}{Knoppix}).  The
-  interesting part for biologists is that Quantian contains in
-  addition all interesting packages of \DebianMed.  The author Dirk
-  Eddelbuettel, who is a Debian developer himself, just used the
-  simply to install biological software feature we provide and thus
-  made a great profit from \DebianMed.
-
-\item[Vigyaan - the biochemical software workbench]
-
-  \halfsloppy\printurl{www.vigyaancd.org}{Vigyaan} is an electronic
-  workbench for bioinformatics, computational biology and
-  computational chemistry.  It has been designed to meet the needs of
-  both beginners and experts.  VigyaanCD is a live Linux CD containing
-  all the required software to boot the computer with ready to use
-  modelling software.  VigyaanCD v0.1 is based on Knoppix v3.3.
-
-  Vigyann contains some programs which are not yet contained in
-  Debian.  It might be mutually beneficial to include these provided
-  that the license fits the DFSG.
-
-\item[BioKnoppix]
-
-  \printurl{bioknoppix.hpcf.upr.edu}{BioKnoppix} is a customised
-  distribution of Knoppix Linux Live CD.  It is a very similar project
-  to the previous which specialises Knoppix for computational biology
-  and chemistry.
-
-\item[VLinux Bioinformatics Workbench]
-
-  Also \printurl{bioinformatics.org/vlinux}{VLinux} is at the time of
-  writing a Live CD based on the same outdated Knoppix version 3.3 as
-  Vigyann and includes a slightly changed software selection and
-  surely a different background layout.
-
-\end{description*}
-
-These are too many different initiatives that could all well do much
-more in order to share the burden of maintenance and updates. With
-Debian they have he right basic infrastructure. The time will show,
-whose packages will gain most momentum.
-\fi
-
 In 2003 to 2005 the advent of several adapted distributions with a
 focus on bioinformatics and medicine could be observed.  Most of them
 were Knoppix\cite{knopper:2005} (and thus indirectly Debian) based.


