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<define-tag pagetitle>What is new for Debian Med in Lenny?</define-tag>
<define-tag release_date>2009-02-15</define-tag>
#use wml::debian::news
# $Id$
<p>
We are proud to announce the first release of Debian Med together with
<q>Lenny</q>, the new <a href="/releases/stable">stable</a> version of the
Debian operating system.
</p>
<p>
The <a href="https://www.debian.org/devel/debian-med/">Debian Med</a> project
continues its <q>healthy</q> growth, which is reflected in a <a
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
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> are 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="https://packages.debian.org/lenny/aeskulap">Aeskulap</a>, <a
href="https://packages.debian.org/lenny/amide">AMIDE</a>, <a
href="https://packages.debian.org/lenny/dicomnifti">dinifti</a>, <a
href="https://packages.debian.org/lenny/fslview">FSLview</a>, <a
href="https://packages.debian.org/lenny/imagej">ImageJ</a>, <a
href="https://packages.debian.org/lenny/python-nifti">PyNIfTi</a>. Thanks to a patch
allowing the use of MySQL 5, we could continue to distribute <a
href="https://packages.debian.org/lenny/ctn">CTN</a> in Lenny. <a
href="https://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"><code>med-imaging</code></a>
package.
</p>
<h2>Sequence analysis and bioinformatics</h2>
<p>
This release saw the arrival in Debian of <a
href="https://packages.debian.org/lenny/emboss">EMBOSS</a>, a very
comprehensive suite of software for sequence analysis, with one of its web
interfaces, <a href="https://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="https://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="https://packages.debian.org/lenny/clustalw">Clustal W</a> is substituted
by <a href="https://packages.debian.org/lenny/kalign">Kalign</a>.
</p>
<p>
This first release of Debian Med addresses some very medical field of
structural bioinformatics. The <a
href="https://packages.debian.org/lenny/autodock">AutoDock</a> suite has arrived
that allows to evaluate metabolites for their affinity to protein receptors,
the basis for <em>in silico</em> drug screening. Debian Med also references further
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"><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="https://packages.debian.org/lenny/pondus">Pondus</a>), software to study
the spread of epidemic diseases (<a
href="https://packages.debian.org/lenny/epigrass">Epigrass</a>), and programs
for organizing the professional work of medical doctors
(<a href="https://packages.debian.org/lenny/gnumed-client">GNUMed</a>). The
<a href="https://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"><code>med-practice</code></a>,
<a href="http://debian-med.alioth.debian.org/tasks/epi"><code>med-epi</code></a>, and
<a href="http://debian-med.alioth.debian.org/tasks/tools"><code>med-tools</code></a>
packages.
</p>
|
