[Cdd-commits] r1169 - projects/med/trunk/papers/09_osehc_porto
CDD Subversion Commit
noreply at alioth.debian.org
Wed Oct 29 21:04:19 UTC 2008
Author: tille
Date: Wed Oct 29 21:04:18 2008
New Revision: 1169
Modified:
projects/med/trunk/papers/09_osehc_porto/paper-text.tex
Log:
Comparison with other repositories
Modified: projects/med/trunk/papers/09_osehc_porto/paper-text.tex
==============================================================================
--- projects/med/trunk/papers/09_osehc_porto/paper-text.tex (original)
+++ projects/med/trunk/papers/09_osehc_porto/paper-text.tex Wed Oct 29 21:04:18 2008
@@ -281,8 +281,7 @@
\section{Results}
-\subsection{Bioinformatics and Debian-associated repositories}
-
+\subsection{Comparable Debian-associated repositories}
\begin{description}
@@ -302,51 +301,25 @@
and perhaps commercial derivatives which might differ in certain
aspects.
- The packages are not, however, core Debian packages. Please read the
- notes below for further details about Bio-Linux packages. They add
- the following notes:
-
- \begin{enumerate}
- \item \sloppy {\em All} of the packages have a dependency on the package
- \package{bio-linux-base-directories}, as this is the package that
- sets up the directory structure and dependencies of several of the
- Bio-Linux system packages. This creates a number of directories
- and configuration files for Bio-Linux but will NOT overwrite
- anything on your system. Therefore you may wish to install this
- package first, or force the install of other packages if you do
- not want to install this package.
- \item {\em Warning}: The \package{bio-linux-bldp-files} package
- contains files which install to a folder called
- \Path{/var/www/boinformatics}. Thus, please ensure that you do
- not already have a directory on your system of this name, or that,
- at the very least, you are not concerned with overwriting any
- index.html file in such an existing directory.
- \item All packages install to \Path{/usr/local/bioinf} and create
- symlinks in \Path{/usr/local/bin} with the exception of the
- bio-linux-genespring software which installs to
- \Path{/home/db/SiliconGenetics} (for more information regarding
- installation of GeneSpring, see our
- \printurl{envgen.nox.ac.uk/sg.html}{GeneSpring Web Page}.)
- \item \halfsloppy \package{Bio-linux-base-directories} installs two
- files into \Path{/usr/local/bioinf/config\_files} (\Path{bioenvrc}
- and \Path{aliasrc}). The file {\em \Path{bioenvrc} should be
- sourced\/} by your shell if you want to pick up the correct
- environmental variables for the software. We recommend the use of
- the
- \printurl{envgen.nox.ac.uk/envgen/software/archives/000499.html\#shells}{z-shell
- for Bio-Linux}. You will also want to \command{source aliasrc}
- if you wish to run some of the Java based software - for example
- \command{maxdView}, \command{maxdLoad2}, \command{mesquite},
- \command{forester}, etc. You will {\em also need to edit} the
- \Path{aliasrc} file to reflect the location of the Java binaries
- on your system.
- \end{enumerate}
-
- The authors did a great job in collecting a certain amount of very
- useful software for biologists and the \DebianMed project might try
- to include some packages which are not yet available in Debian
- officially.
-
+ 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]
@@ -373,14 +346,23 @@
Packages for multiple distributions are provided, which includes
Debian, and a live CD.
-\item[bioinformatics.debian.net]
+\end{description}
+
+\subsection{Other repositories of biology related software}
- Debian developer Matt Hope has created a small set of packages for
- Debian that he has not yet uploaded to the main distribution.
- Most are in a very nice state he just should submit.
+Looking beyond Debian and related distributions which share more or
+less the same technique we find similar efforts to deliver sets of
+ready to install software
-\end{description}
+\begin{description}
+\item[FreeBSD Ports: Biology] The Free Software world does not only
+ know Linux as free operating system. There are others out there
+ like several BSD derivates, OpenSolaris, Hurd and others. The
+ FreeBSD project has a really nice
+ \printurl{http://www.freebsd.org/ports/biology.html}{collection of
+ biological software}.
+\end{description}
\subsection{Bioinformatics Live CDs}
@@ -393,7 +375,6 @@
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]
@@ -430,13 +411,11 @@
\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
@@ -446,15 +425,34 @@
\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.
-
-
-\subsection{Bioinformatics and \DebianMed}
+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.
+
+
+\subsection{Comparison with \DebianMed}
+
+Looking at all the projects above it becomes evident that they are all
+dealing only with biological software. Above it was stated that one
+strong column of \DebianMed is this specific field and it is for a
+reason: The amount of free biological software is large and most of
+these projects are relatively easy to turn into packages - so the
+amount of work per package is much smaller compared to for instance
+medical record applications with preparation of databases, dedicated
+user management, etc.
+
+So there is one major difference between the projects mentioned above
+and \DebianMed: While the biological part is really interesting for
+medical care \DebianMed tries to cover all other fields of medical
+care as well. This goal is not yet reached but continuous work is
+done into this direction and some important steps are done.
+
+An even more important difference than the more general approach of
+\DebianMed is the fact that \DebianMed is not only about just
+packaging software.
-\DebianMed is a Custom Debian Distribution with the aim to develop
+\DebianMed is a Debian Pure Blend with the aim to develop
Debian into an operating system that is particularly well fit for the
requirements for medical practice and research. The goal of \DebianMed
is a complete system for all tasks in medical care which is build
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