[Cdd-commits] r1173 - projects/med/trunk/papers/09_osehc_porto
CDD Subversion Commit
noreply at alioth.debian.org
Thu Oct 30 21:06:10 UTC 2008
Author: tille
Date: Thu Oct 30 21:06:09 2008
New Revision: 1173
Modified:
projects/med/trunk/papers/09_osehc_porto/paper-text.tex
Log:
Send it in for review now
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 Thu Oct 30 21:06:09 2008
@@ -22,6 +22,7 @@
Edu, Debian Science and others.
\end{abstract}
+\subsubsection*{List of abbreviations}
\begin{tabular}{ll} % to become llll later
Blend & Debian Pure Blend \\
BTS & Bug Tracking System \\
@@ -567,6 +568,7 @@
\caption{Activity of most active authors on the \DebianMed mailing list}\label{figure:authorstats}
\end{figure*}
+\enlargethispage{10mm}
This growth of the output of a project is an important part but
we also try to measure the commitment of the people involved in the
project. It has to be ensured that fresh blood is flooding into the
@@ -623,17 +625,6 @@
to new members and to external sites offering packages for
installations.
-From the perspective of data security it should be stressed that
-Debian GNU/Linux has the unique feature of the automated creation of
-\command{chroot} environments. In a dedicated directory, the minimal
-set of programs is stored to run a a Debian GNU/Linux system. A
-process started in such will not have file access to the remainder of
-the system with otherwise complete functionality. The process is
-separated, even when started as root. Hence, arbitrary packages can be
-added and computations performed, be it for the build daemon or
-others, without accidentally or intentionally impeding the functioning
-of the underlying operating system.
-
\subsection{Differences from other distributions}
@@ -641,9 +632,9 @@
ways. Firstly, Debian is a non-commercial organisation of volunteers,
that does not sell anything. The second and most appealing difference
is the peer review and continuous pressure among the members to
-provide a high quality of packages. The Debian society has a constitution,
-elects its leader, and transparently describes policies for the
-creation of packages utilising specific technologies.
+provide a high quality of packages. The Debian society has a
+constitution, elects its leader, and transparently describes policies
+for the creation of packages utilising specific technologies.
With these principles, Debian achieved the largest collection
of ready-to-install Free Software on the Internet.
@@ -654,12 +645,11 @@
Several existing programs that might be useful for specialists are not
free in the sense of the
\printurl{www.debian.org/social\_contract\#guidelines}{Debian Free
- Software Guidelines} \cite{dfsg}.
-Programs that are incompatible with the
-DFSG cannot be included in the Debian main distribution.
-One famous example of this group
-is \printurl{evolution.genetics.washington.edu/phylip.html}{PhyLip}
-and the same hold for ClustalW. Both programs' licenses contain a clause
+ Software Guidelines} \cite{dfsg}. Programs that are incompatible
+with the DFSG cannot be included in the Debian main distribution. One
+famous example of this group is
+\printurl{evolution.genetics.washington.edu/phylip.html}{PhyLip} and
+the same hold for ClustalW. Both programs' licenses contain a clause
like
\begin{quote}
Permission is granted to copy and use this program provided no fee
@@ -667,14 +657,15 @@
removed.
\end{quote}
As a consequence no reseller of Debian would be allowed to sell Debian
-because one CD contains PhyLip.
-Hence, this program may not be redistributed per default with the main
-and essential tools of Debian. Problems are, starting with those for the user:
+because one CD contains PhyLip. Hence, this program may not be
+redistributed per default with the main and essential tools of
+Debian. Problems are, starting with those for the user:
\begin{itemize}
\item Need to obtain PhyLip from a different source
\item If the user is not using a "common" architecture like {\ttfamily
i386} he might run into problems in compiling the latest version
- as only the packages of the main distribution are submitted to the build daemons to save resources.
+ as only the packages of the main distribution are submitted to the
+ build daemons to save resources.
%\item No extra security checks from his trusted operating system vendor.
\item The user might not even notice that something like PhyLip exists
at all. \DebianMed cares for pointing users to relevant software
@@ -683,7 +674,7 @@
research.
\end{itemize}
-%While Debian Med supperts packages in the non-free section of
+%While Debian Med supports packages in the non-free section of
%Debian this might be dropped at any time and has certain constraints.
From the developers point of view we face also drawbacks:
\begin{itemize}
@@ -695,9 +686,9 @@
\end{itemize}
While every author is perfectly free to choose this kind of license,
-Free Software experts agree that this kind of restrictions is
-possibly a drawback for those programs because they do not fully use
-the spinning power of Free Software development.
+Free Software experts agree that this kind of restrictions is possibly
+a drawback for those programs because they do not fully use the
+spinning power of Free Software development.
\subsubsection{Importance of community support}
@@ -722,11 +713,17 @@
Debian developers can provide packages which are checked and
uploaded by official maintainers. There is no point in keeping good
quality softwares outside of Debian.
+\item \printurl{http://debian-med.alioth.debian.org/tasks/}{The tasks
+ page of \DebianMed} mentioned above does not only contain the work
+ that was done -- it contains also a nicely formated list which
+ projects would be interesting to reach the final goal to cover each
+ task in medical care with Free Software. This list inside each
+ section might give some idea where help might be needede.
\item \halfsloppy Verify whether one needs special configuration for
your project. If yes, verify which possibilities are given in the
- Custom Debian Distribution effort. It is more than collecting
- software but bringing the software to your target users while taking
- the burden from any configuration issues from his back.
+ Debian Pure Blends effort. It is more than collecting software but
+ bringing the software to your target users while taking the burden
+ from any configuration issues from his back.
\item The only reason to keep things outside of Debian are licenses
which are not compatible with DFSG. All other parts of your
projects can be included and your time for everyday package building
@@ -734,55 +731,24 @@
following the same road.
\end{enumerate}
-There are two ways to obtain Debian GNU/Linux:
-\begin{enumerate}
-\item Installation from a CD that may be borrowed from a friend, or
- bought from a commercial vendor. This may be together with a
- computer magazine on a newsstand or from a redistributor on the
- Internet.
-\item Download Debian from the web for free from a local mirror.
-\end{enumerate}
-
-The latter is the common way, a net install will only download the
-required packages.
-
-
-\subsubsection{Biological databases}
-
-The Debian community has yet not addressed the problem of
-incorporating biological databases into Debian. It seems not likely
-that this will happen in the Debian main distribution. The extra
-burden to maintain copies of e.g. the EMBL DNA sequence database on
-multiple mirrors of Debian puts too much of a burden to the mirrors
-with only little gain. And not everybody requires regular updates
-with the associated network traffic and the induced instability when
-exchanging the files while scripts might still be running reading the
-data. The provision of a set of tools that provides updates on demand
-seems a more likely scenario. This would then also need to manage the
-update of indices of e.g. sequence similarity tools.
-
-For now, Debian offers libraries like BioPerl with its facility to
-access online repositories, circumventing problems with the updating
-of local data. Debian is well suited though to address the issue
-because of its means of introspection, the programmer can tell which
-databases are installed and what files are available.
-
\section{Conclusions}
We have shown that there is a considerable heterogeneous shape of Free
-Software in biology. The continuous updates of data and the addition of
-novel important tools for a general bioinformatics environment cannot
-be performed by a single maintainer. The adherence to a policy and the
-sharing of maintenance are basic technologies to allow
-inter-institutional software projects of different kind in health care.
-
-Debian and its special dedication to software in computational biology
-in \DebianMed, but also the technical infrastructure behind this
-community project renders a comfortable solution. The volunteers
-behind \DebianMed strive to support everybody's specific projects as
-best as they possibly can. It is the particular challenge of users of
-Free Software, to determine together with the community the available
+Software for medical care even if some fields like micro biology are
+better covered than others. The continuous updates of data and the
+addition of novel important tools for a general medical environment
+cannot be performed by a single maintainer. The adherence to a policy
+and the sharing of maintenance are basic technologies to allow
+inter-institutional software projects of different kind in health
+care.
+
+Debian and its special dedication to medical software in \DebianMed,
+but also the technical infrastructure behind this community project
+renders a comfortable solution. The volunteers behind \DebianMed
+strive to support everybody's specific projects as best as they
+possibly can. It is the particular challenge of users of Free
+Software, to determine together with the community the available
packages that already serve their needs or may be adapted
respectively.
@@ -793,12 +759,12 @@
like for instance OpenVista\cite{openvista:2008} and other enterprise
grade health care information systems has to be packaged for Debian.
-Whatever choice for an infrastructure is made, with Debian it is available
-to all collaborating sites almost instantly.
+Whatever choice for an infrastructure is made, with Debian it is
+available to all collaborating sites almost instantly.
\subsection*{Acknowledgements}
-The authors thank the Debian Developers for all their work and
+The author thanks the Debian Developers for all their work and
particularly those who have contributed to \DebianMed and the Debian
Pure Blends effort which builds a common framework around similar
projects like Debian Edu for education, Debian Science for scientific
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