Category Archives: distributions

Debian-Med Distribution Project Announced

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.