[med-svn] r5598 - in trunk/community/papers: . 11_med-floss_luxemburg
Andreas Tille
tille at alioth.debian.org
Fri Dec 10 21:16:32 UTC 2010
Author: tille
Date: 2010-12-10 21:16:27 +0000 (Fri, 10 Dec 2010)
New Revision: 5598
Modified:
trunk/community/papers/11_med-floss_luxemburg/paper-text.tex
trunk/community/papers/debian-med.bib
Log:
Trying final polishing with resolving comments or keeping them with additions for further enhancements
Modified: trunk/community/papers/11_med-floss_luxemburg/paper-text.tex
===================================================================
--- trunk/community/papers/11_med-floss_luxemburg/paper-text.tex 2010-12-10 13:51:27 UTC (rev 5597)
+++ trunk/community/papers/11_med-floss_luxemburg/paper-text.tex 2010-12-10 21:16:27 UTC (rev 5598)
@@ -104,24 +104,14 @@
\subsection{Status of Free Software in health care}
-More common programs like a web server, or a mail user agent are installed
-on a vast amount of computers and have a very large user base.
-% that might be a little far fetched
-%This increases the chance to
-%attract gifted programmers who could have an almost intuitive spontaneous
-%understanding on the structure of the control flow of the program
-%(by understanding the problem domain extremely well) and could map
-%this to the source code (since they would have solve the problem
-%in a similar way).
-A large use base, in turn increases the likelihood of attracting skilled
-programmers that tackle unresolved problems or general improvements of the
-software they are using.
-This type of user is extremely valuable to a project, because they can
-implement and contribute any modification they need by themselves without having to rely
-on a project's manpower.
-%For the
-%larger challenges there may be many different driving forces coming
-%together. \marginpar{explain?}
+More common programs like a web server, or a mail user agent are
+installed on a vast amount of computers and have a very large user
+base. A large use base, in turn increases the likelihood of
+attracting skilled programmers that tackle unresolved problems or
+general improvements of the software they are using. This type of
+user is extremely valuable to a project, because they can implement
+and contribute any modification they need by themselves without having
+to rely on a project's manpower.
The fact that a piece of software is needed for one's own work is often
the basic motivation to write Free Software. Biological software is
@@ -189,12 +179,9 @@
The Debian Project is an association of individuals who share the
intention to create the best possible free operating system. This
-operating system is called Debian GNU/Linux, or simply
-Debian. Everybody on the Internet may initiate a site and
-offer Debian packages.
-% this topic doesn't fit here
-%A local administrator
-%has to decide, if this public source may be trusted.
+operating system is called Debian GNU/Linux, or simply Debian.
+Everybody on the Internet may initiate a site and offer Debian
+packages.
To make Free Software development work, it requires a critical mass of
supporters. Development without feedback prior to the submission of
@@ -252,12 +239,17 @@
do-ocracy} in Debian and refers to the fact that: the one who does something
decides what is done and how it is done.
-% Is this needed?
-%Usually, maintainers
-%choose software that they use for their professional work, for those
-%who use Linux at work. And they are free
+%% FIXME
+%% at: add a more detailed explanation why I finally think that this
+%% paragraph should be kept - but leave it for later versions of
+%% this document
+%Usually, maintainers choose software that they use for their
+%professional work, for those who use Linux at work. And they are free
%to move the development of Debian in a certain direction (as long as
-%they follow the rules of the policy).
+%they follow the rules of the policy). For Free Medical Software this
+%means that in most cases the developers are health care professionals
+%or IT experts working in health care and they just merge their
+%professional interest into the progress of Debian.
\subsubsection{Active influence of small groups}
@@ -290,21 +282,18 @@
\subsubsection{Bug tracking system}
-Users should be able to give immediate feedback about problems affecting a
-software. While they always have the choice of reporting these to the
-upstream developer, usually per email,
-%A particular strength of
-%\printurl{www.sourceforge.net}{SourceForget.net} is to bring users of
-%a particular software together.
-%Earlier than this effort was
-the \printurl{www.debian.org/Bugs}{Debian Bug Tracking System} (BTS) offers
-an additional channel for tracking software defects efficiently. The
-maintainer of a piece of software can investigate whether a particular report is actually
-valid before upstream developers need to deal with it. Moreover, in many cases
-the Debian maintainer can suggest or even implement fixes, that are then sent
-to upstream alongside the bug report, if the problem is not Debian-specific.
-All problems are made public, and hence the whole community
-may contribute to solving a particular issue.
+Users should be able to give immediate feedback about problems
+affecting a software. While they always have the choice of reporting
+these to the upstream developer, usually per email, the
+\printurl{www.debian.org/Bugs}{Debian Bug Tracking System} (BTS)
+offers an additional channel for tracking software defects
+efficiently. The maintainer of a piece of software can investigate
+whether a particular report is actually valid before upstream
+developers need to deal with it. Moreover, in many cases the Debian
+maintainer can suggest or even implement fixes, that are then sent to
+upstream alongside the bug report, if the problem is not
+Debian-specific. All problems are made public, and hence the whole
+community may contribute to solving a particular issue.
In the case of Free Medical Software the upstream projects frequently
do not feature a bug tracking system. Thus the inclusion of such
@@ -359,11 +348,7 @@
Debian contains more than 20,000 binary packages, and this number is
constantly increasing. There is no single user who needs all these
-packages.
-% duplication
-%The typical user is interested in a subset of these
-%packages.
-To specify packages of one's particular interest, several
+packages. To specify packages of one's particular interest, several
options are provided by Debian:
\begin{description*}
@@ -374,9 +359,6 @@
will support \command{tasksel} to enable selection of \emph{niche}
software collections, \emph{e.g.} \DebianMed, right after a fresh installation of a
general Debian system.
-% yoh: don't we want ideally "during a fresh installation of a Debian system"?
-% at: we would *want* this but unfortunately we would need our own
-% adapted ISO image to approach this
\item[command line package management] \command{apt} and \command{aptitude} provide means to
search for packages of particular interest by name or words in
@@ -388,7 +370,7 @@
% yoh: what about
% debtags + axi-cache (at)
% "Similar packages" on packages.debian.org?
-% at: yes, needs to be added here and also in Blends documentation
+% at: yes, needs to be added here and also in Blends documentation (FIXME)
\item[GUI] There are several graphical user interfaces to manipulate
the installation of packages on a Debian system. The most
@@ -404,6 +386,7 @@
\emph{i.e.} Fink on Mac OS X
(\printurl{fink.sourceforge.net}{fink.sourceforge.net}).
+% FIXME
% yoh: context below is not necessary about GNU and even more so
% not about Linux
% MH: agreed, and moreover if that is mentioned somewhere it should move to
@@ -608,17 +591,17 @@
molecular biology and medical genetics and others.
%% This sounds somewhat redundant to me - SM
-Each field of work has an appropriate metapackage, for instance
-\package{med-bio} for packages concerning molecular biology and
-medical genetics and \package{med-practice}, which is helpful to
-manage a medical practice. The sense of using metapackages is that you
-have to install only a single package using a package management
-software tool to get all interesting packages that are
-necessary for a single task. For
+Technically these categories are implemented as appropriate
+metapackages, for instance \package{med-bio} for packages concerning
+molecular biology and medical genetics and \package{med-practice},
+which is helpful to manage a medical practice. The sense of using
+metapackages is that you have to install only a single package using a
+package management software tool to get all interesting packages that
+are necessary for a single task. For
instance a single command \\
\hspace*{10mm}\texttt{apt-get install med-bio} \\
-results in installation of all applications inside Debian that are related to the field of
-molecular biology and medical genetics.
+results in installation of all applications inside Debian that are
+related to the field of molecular biology and medical genetics.
\subsubsection{Continuous growth}
@@ -651,43 +634,54 @@
spirit of open source. As a result, anyone
interested can easily contribute and acceptance might be only a couple of emails away.
+% FIXME
% Should the Google Code-In and Google Summer of Code be mentioned?
% What else would we have than those Google activities?
% BOSC comes to mind, presentations on FOSDEM etc. Make a paragraph
% of it if you like.
-%
-%Debian is a continuous contributor to
+
+%% FIXME
+%% sm: one should not say something negative about someone else if
+%% that is avoidable
+%% at: I regard this a {\bf really burning} problem which we need
+%% to address in a paper. It is not negative to express an
+%% observation
+Several Free Software projects which try to deal with small user group
+software started with a lot of enthusiasm but at some point in time
+developers had other interests or changed their job. There are just
+several reasons why people are not able to continue maintenance of a
+project because of lack of man power.
-%% one should not say something negative about someone else if
-%% that is avoidable
-%Several Free Software projects which try to deal with small user group
-%software started with a lot of enthusiasm but at some point in time
-%developers had other interests or just were unable to maintain the
-%project because of lack of man power.
+%% FIXME
+%% sm: This "within debian" could be interpreted negatively
+%% at: why? I think we should not hide the reason why \DebianMed
+%% is successful.
+To make sure the manpower of the team can fully concentrate on the
+field of work they really want to do the strategy of \DebianMed is
+to stay strictly inside Debian -- so even if the team started with
+a few people they were able to relay on a solid technical basis
+without extra effort.
-%% This "within debian" could be interpreted negatively
-%The strategy of \DebianMed is
-%to stay strictly inside Debian -- so even if manpower is a problem
+Thus \DebianMed is not a derived distribution and is a part of the
+Debian project. \DebianMed relies on the core Debian infrastructure
+(\emph{e.g.} build farm for a variety of architectures, online
+repositories and mirrors, bug tracking system) and only complements it
+with an additional thin layer yet again functioning within Debian
+infrastructure. That guarantees that the overall development system
+remains robust and does not require extra effort from the \DebianMed
+sub-community. Moreover, adherence to common principles and
+organisation helps \DebianMed project members to improve efficiency
+and share overall maintenance cost because many actions can be
+performed on the entire pool of maintained packages at once.
+Admittedly, quite frequently software products maintained by
+\DebianMed are of generic utility, such as Java or Python libraries,
+and thus of interest to the Debian audience outside of the target
+scope of \DebianMed -- Medicine, as a result benefiting Debian as a
+whole.
+% Due to significant overlap, boundaries between different
+%Blends are not clearly defined and the separation of \DebianMed from
+%\emph{e.g.} Debian Science is often artifactual.
-\DebianMed is not a derived distribution and is a part of the
-Debian project. \DebianMed relies on the core Debian infrastructure (\emph{e.g.} build farm
-for a variety of architectures, online repositories and mirrors, bug
-tracking system) and only complements it with an additional thin
-layer yet again functioning within Debian infrastructure.
-That guarantees that the overall development system remains robust
-and does not require extra effort from the \DebianMed sub-community.
-Moreover, adherence to common principles and organisation
-helps \DebianMed project members to improve efficiency and share
-overall maintenance cost because many actions can be performed on the
-entire pool of maintained packages at once. Admittedly, quite
-frequently software products maintained by \DebianMed are of generic
-utility, such as Java or Python libraries, and thus of interest to the
-Debian audience outside of the target scope of \DebianMed -- Medicine,
-as a result benefiting Debian as a whole. Due to significant
-overlap, boundaries between different Blends are not clearly defined and
-the separation of \DebianMed from \emph{e.g.} Debian Science is often
-artifactual.
-
\begin{figure}[!htp]
\centering
\myinsertgraphic{authorstat.pdf}{100mm}{60mm}
@@ -720,8 +714,16 @@
% increases, email traffic decreases -- more efficient - more
% work, less words), or plot should be different to show actually
% a number of mailing lists participants
+% at: We have a lot of projects where the flow of developers is way
+% heavier and they actually lose developers. We also lost one
+% of the most active posters and thus it is rather 9 despite
+% initial selection.
% I would not show that
+% at: I have heard the opinion that specifically that is important
+% for "real" work: I'm the most active "chatter" (on debian-med)
+% but Charles is much more busy in working (on the development
+% lists - so I think we should leave this
Considering that some technical discussions initiated at \DebianMed
mailing lists quite often naturally migrate to the packaging
list (see Figure \ref{figure:develstats}(a)) the number of postings of
@@ -782,7 +784,9 @@
covered by \DebianMed. The list of all the packages is regenerated
on a daily basis and includes some meta information to \emph{e.g.} point to
relevant scientific publications and the description of the
-packages in this task. The output of the project can be easily \marginpar{just have a regular reference to the URL}
+packages in this task. The output of the project can be easily
+% FIXME at: I just don't understand this remark
+% \marginpar{just have a regular reference to the URL}
viewed at \printurl{debian-med.alioth.debian.org/tasks/}{the
tasks page of \DebianMed}.
@@ -826,11 +830,14 @@
and shares its developments across platforms.
+%% FIXME
+%% Can this subsection go? openSUSE I do not know, but at least
+%% Fedora is just plain excellent in exactly that, too, and it
+%% has some other principles from which Debian can learn, still.
+%% at: I agree that the content of this paragraph is from pre-Fedora
+%% ages. I in principle like to propagate the idea but we
+%% need better wording - so drop it for the moment
%
-% Can this subsection go? openSUSE I do not know, but at least
-% Fedora is just plain excellent in exactly that, too, and it
-% has some other principles from which Debian can learn, still.
-%
%\subsection{Other distributions}
%
%The Debian GNU/Linux distribution differs from others in several
@@ -847,18 +854,18 @@
%
% Could we say what needs to be said here somewhat earlier, possibly?
-% I am not sure I want BioLinux to be mentioned in this way, with
+% I am not sure I want Bio-Linux to be mentioned in this way, with
% whom an active bidirectional collaboration is only developing now
\subsubsection{Importance of community support}
That strong support within the community of users is essential for the
development of software, for quality assurance, feedback on features,
and not at least for the motivation of staff, that all commercial
-distributors are well aware of. For example, Red Hat has initiated Fedora as
-a free supplement to their commercial distribution. This is the reason
-why \DebianMed is part of Debian and why groups external to the Debian
-society, like BioLinux\marginpar{ref for BioLinux}, are also keen on close collaboration with the
-community.
+distributors are well aware of. For example, Red Hat has initiated
+Fedora as a free supplement to their commercial distribution. This is
+the reason why \DebianMed is part of Debian and why groups external to
+the Debian society, like Bio-Linux\cite{biolinux:2010}, are also keen
+on close collaboration with the community.
\subsubsection{Approaching \DebianMed}
Modified: trunk/community/papers/debian-med.bib
===================================================================
--- trunk/community/papers/debian-med.bib 2010-12-10 13:51:27 UTC (rev 5597)
+++ trunk/community/papers/debian-med.bib 2010-12-10 21:16:27 UTC (rev 5598)
@@ -269,6 +269,13 @@
URL="http://www.bioimagesuite.org/"
}
+ at ARTICLE{biolinux:2010,
+ AUTHOR="{NERC Environmental Bioinformatics Centre}",
+ TITLE="{Bio-Linux}",
+ YEAR="2010",
+ URL="http://envgen.nox.ac.uk/tools/bio-linux"
+}
+
@ARTICLE{gnumed:2008,
AUTHOR="Karsten Hilbert",
TITLE={{GNUmed}},
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