Re: Roadmap to Lenny: news release draft.

[Andreas Tille <tillea@rki.de>]

On Sat, 14 Feb 2009, Charles Plessy wrote:

> After a five-month lapse, I tried to finish the redaction of the news for the
> release of Debian Med for Lenny. I attached the WML source to this email.

Many thanks for working on this.  I'd like to comment as usual quotes
(because I have no idea whether you kept the text in SVN somewhere)


>   href="dmstats1.pdf">continuous increase of packages for medical care</a> and <a
>   href="authorstat_med.pdf">an increasing number of people</a> who are actively

Do you intend to copy dmstats1.pdf and authorstat_med.pdf to devel/debian-med
or would you use explicite links?  Currently the links are not working.

>   working on the project. Our current work is concentrated in our three main
>   areas of activity: imaging, bioinformatics, and medical practice. During this
>   release cycle, we developed new dynamic web pages to present the content of
>   our meta-packages, organised in <q><a

Please always use the spelling "metapackages" (without '-').  This is
the spelling our native English speakers agreed to.

Moreover the pages are actually not really "dynamic" - these are static
HTML pages generated twice a day.
>   href="http://debian-med.alioth.debian.org/tasks/";>tasks</a></q>.
> </p>

My suggestion for this paragraph would be:

   working on the project. Our current work is concentrated in our three main
   areas of activity: imaging, bioinformatics, and medical practice. During this
   release cycle, we developed <a
   href="http://debian-med.alioth.debian.org/";>new dynamic web pages</a>
   to present the development status of our project.
 </p>
 <p>
   The so called <a href="http://debian-med.alioth.debian.org/tasks";>task
   pages</a> might be the most interesting entry point for users or
   potential users of Debian Med because they reflect the current
   status of our work regarding integration of medical software into
   Debian.  The <a href="http://debian-med.alioth.debian.org/tasks";>task
   pages</a> provide a list of ready to install medical software and
   moreover a contact point for users who might need a certain program
   which is not yet available.  If something is missing on the list
   of available software users might ask us for missing things or can
   easily obtain the status of work on a project.
 </p>
 <p>
   In addition to the user oriented tasks pages we also generate
   pages which show the bugs concerning the medical software inside
   Debian.  The <a href="http://debian-med.alioth.debian.org/bugs";>bugs
   pages</a> a useful tool for Debian Med developers to see immediately
   which packages need to be worked on.
 <p>

> <h2>Medical imaging</h2>
>
> <p>
>   Many new packages were made for programs supporting the <a
>   href="http://en.wikipedia.org/wiki/DICOM";>DICOM</a> and Nifti formats, that
>   are important standards in the field of medical imaging: <a
>   href="http://packages.debian.org/lenny/aeskulap";>Aeskulap</a>, <a
>   href="http://packages.debian.org/lenny/amide";>AMIDE</a>, <a
>   href="http://packages.debian.org/lenny/dicomnifti";>dinifti</a>, <a
>   href="http://packages.debian.org/lenny/fslview";>FSLview</a>, <a
>   href="http://packages.debian.org/lenny/imagej";>ImageJ</a>, <a
>   href="http://packages.debian.org/lenny/python-nifti";>PyNIfTi</a>. Thanks to a patch
>   allowing the use of MySQL&nbsp;5, we could continue to distribute  <a
>   href="http://packages.debian.org/lenny/ctn";>CTN</a> in Lenny. <a
>   href="http://packages.debian.org/sid/ctsim";>CTSIM</a>, which depends on an old
>   version of the WxWidgets library, will not be part of the release, but it
>   will nevertheless stay part of Debian in the unstable section. Once upgraded
>   to a more recent version of WxWidgets, the Debian Med project will prepare an
>   official <a href="http://backports.org";>backport</a>.
> </p>
>
> <p>
>   You can find all the programs for medical imaging in our
>   <a
>   href="http://debian-med.alioth.debian.org/tasks/imaging.html";><code>med-imaging</code></a>
>   package.
> </p>
>
>
> <h2>Sequence analysis and bioinformatics</h2>
>
> <p>
>   This release saw the arrival in Debian of <a
>   href="http://packages.debian.org/lenny/emboss";>EMBOSS</a>, a very
>   comprehensive suite of software for sequence analysis, with one of its web
>   interfaces, <a href="http://packages.debian.org/lenny/emboss-explorer";>EMBOSS
>   Explorer</a>, that you can use locally, on your intranet or on the Internet
>   after an installation as simple as typing <q><code>aptitude install
>   emboss-explorer</code></q>.
> </p>
>
> <p>
>   Debian Med now distributes all the major free programs for multiple sequence
>   alignment. One of them, <a
>   href="http://packages.debian.org/lenny/t-coffee";>T-Coffee</a>, can function as
>   a meta-aligner (<q>M-Coffee</q>), that runs multiple programs and combines
>   their outputs in a higher-quality alignment. Its author kindly developed a
>   version that only depends on free software, <q>DM-Coffee</q>, in which <a
>   href="http://packages.debian.org/lenny/clustalw";>Clustal&nbsp;W</a> is substituted
>   by <a href="http://packages.debian.org/lenny/kalign";>Kalign</a>.
> </p>
>
> <p>
>   This first release of Debian-Med addresses some very medical field of

s/Debian-Med/Debian Med/

>   structural bioinformatics. The <a
>   href="http://packages.debian.org/lenny/autodock";>AutoDock</a> suite has arrived
>   that allows to evaluate metabolites for their affinity to protein receptors,
>   the basis for in silico drug screening. Debian-Med also references further

s/Debian-Med/Debian Med/

>   structural packages that are provided by the Debian Science community like
>   Gromacs or PyMol."
> </p>
>
>
> <p>
>   You can find all the programs for sequence analysis and bioinformatics in our
>   <a
>   href="http://debian-med.alioth.debian.org/tasks/bio.html";><code>med-bio</code></a>
>   package.
> </p>
>
>
> <h2>Diversification of the medical packages.</h2>
>
> <p>
>   Debian Med covers a broad area relevant to medicine, with for instance
>   software for helping people to take care of their health and body (<a
>   href="http://packages.debian.org/lenny/pondus";>Pondus</a>), software to study
>   the spread of epidemic diseases (<a
>   href="http://packages.debian.org/lenny/epigrass";>Epigrass</a>), and programs
>   for organizing the professional work of medical doctors
>   (<a href="http://packages.debian.org/lenny/gnumed-client";>GNUMed</a>). The
>   <a href="http://packages.debian.org/experimental/gnumed-server";>GNUMed
>   server</a> is not yet available as a stable Debian package, but can be found
>   in our experimental section for those who would like to help by testing.
> </p>
>
> <p>
>   You can find all the programs for health and medicine in our
>   <a  href="http://debian-med.alioth.debian.org/tasks/practice.html";><code>med-practice</code></a>,
>   <a  href="http://debian-med.alioth.debian.org/tasks/epi.html";><code>med-epi</code></a>, and
>   <a  href="http://debian-med.alioth.debian.org/tasks/tools.html";><code>med-tools</code></a>
>   packages.
> </p>


Well done job Charles - many thanks!

Kind regards

       Andreas.
--
http://fam-tille.de