Debian-Med Distribution Project Announced

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Debian-Med Distribution Project Announced

Posted by I. Valdes on Tuesday January 08, @01:02AM
from the distributions dept.
Andreas Tille is announcing a medicine oriented Debian distribution project called 'Debian-Med' which '...will have two main components: Support for general practice and laboratory research. The general idea is adopted from the Debian Junior project. So we provide a set of packages which have dependencies from Debian packages which help solve certain tasks.

At first glance I have the following packages in my mind:

For General Practiciants:

- GnuMed http://www.gnumed.org/ There will be ITPs for GnuMed and its tools soon from myself. GnuMed will be a major part of Debian-Med and I will have focus my own packaging work on this project.

- FreePM http://www.freepm.org/ FreePM is an open source physicans office management & electronic medical record application. This is a Zope based project and there are reference implementations. I think it would be worth packaging for Debian.

- Open Infrastructure for Outcomes http://www.txoutcome.org/ Open Infrastructure for Outcomes (OIO) system facilitates the creation of flexible and portable patient/research records. It aims to achieve the "Holy Grail" of data portablity as elegantly described by John G. Faughnan. Another Zope based project.

- FreeMed http://www.freemed.org (seems to be temporarily offline??) Similiar to FreePM but PHP/MySQL based. I personally prefer GnuMed because it uses PostgreSQL and has a clear Client/Server structure but perhaps FreeMed yould be turned into a nice web client to GnuMed.

Microbiology (if there are Debian packages I just name the package URL)

- ncbi-tools6 - NCBI libraries for biology applications http://packages.debian.org/unstable/libs/ncbi-tools6.html (actively maintained by Aaron M. Ucko)

- seaview - A multiple sequence alignment editor http://packages.debian.org/unstable/misc/seaview.html (orphaned)

- clustalw - A multiple sequence alignment program http://packages.debian.org/unstable/science/clustalw.html (maintained by myself)

- phylip - A package of programs for inferring phylogenies. http://packages.debian.org/unstable/misc/phylip.html (maintained by myself)

- treetool - An interactive tool for displaying trees http://packages.debian.org/unstable/science/treetool.html (orphaned)

- molphy - Program Package for MOLecular PHYlogenetics http://www.ism.ac.jp/software/ismlib/softother.e.html (my package is in incoming)

- fastdnaml - A tool for construction of phylogenetic trees of DNA sequences http://packages.debian.org/unstable/science/fastdnaml.html (maintained by myself)

- njplot - A tree drawing program http://packages.debian.org/unstable/science/njplot.html (orphaned)

- readseq - Conversion between sequence formats http://packages.debian.org/unstable/science/readseq.html (maintained by myself)

- tree-puzzle - Reconstruction of phylogenetic trees by maximum likelihood http://packages.debian.org/unstable/science/tree-puzzle.html (maintained by myself)

- ARB http://www.arb-home.de/ Integrated package for data handling and analysis. I have preliminary packages of the recent Beta available. There are several issues to sort out (especially concerning licenses of Arb itself and the tools used by Arb).

Documentation and Research

- BioMail http://www.biomail.org/ Nice if you are seeking for relevant literature. Once there was an ITP for this program by another Debian developer. I builded preliminary packages and suggested some changes upstream to speed up packaging process. The maintainer who wanted to package it seemed to lost interest and so just feel free to take over my preliminary work which needs some cleaning and some discussion with upstream.

- Medicine-HOWTO http://mobilix.org/Medicine-HOWTO.html

Todo-List:

- Project page at debian.org
- Mailing list
- Logo? (Perhaps some skilled painter could take the idea of the GnuMed logo and replace the GNU by the Debian swirl - just an idea)
- Packages ...
- Documentation (including translation)

Further Links:
http://www.linuxmednews.com/projects/
http://www.openhealth.com/en/healthlinks.html
http://www.omp.de.vu (German)

I'm looking foreward for comments, suggestions and most importantly - help!

Kind regards

Andreas.

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