Bioinformatics and Debian-Med

Debian-Med is a Custom Debian Distribution with the aim to develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research. The goal of Debian-Med is a complete system for all tasks in medical care which is build completely on free software.

On the technical side Debian-Med contains a set of meta packages that declare dependencies on other Debian packages, and that way the complete system is prepared for solving particular tasks. A special user menu will be created to enhance usability for the user working in the field of medicine.

On the organisational side the project tries to attract people working in the field of Free Software in medicine to share the effort of building a common platform which reduces the amount of work for developers and users. Sharing the effort in publishing free medical software to a large user base is a main advantage of Debian-Med.

Currently inside Debian-Med applications are provided in certain categories: medical practice and patient management, medical research, hospital information systems, medical imaging, documentation, molecular biology and medical genetics and others. The last part seems to be the most interesting and will be introduced in more detail.

There are two so called meta packages which are named med-bio and med-bio-dev. The sense of a meta package is that you have to install only one single package using a package management software inside Debian to get all interesting packages which are necessary for a single task. For instance if a user types in:
apt-get install med-bio
all applications inside Debian which are related to the field of molecular biology and medical genetics will be installed. Moreover system users will get an extra menu which contains all these applications. The med-bio-dev package just installs programming libraries and tools which are interesting for users who want to develop biological applications (for instance the NCBI library[4,1,3]).

The strength of Debian is the huge number of developers (more than 1000) all over the world working in different fields1. Some of them are working in the field of biology or medicine and thus have a natural interest in developing a rock solid system they can relay on for their own work (not only commercial interest to sell service per accident). That is the reason why Debian is often the platform of choice for researcher in the field of biology: They just find what their colleagues all over the world are using. The more the Debian user in the field of biology report back about problems or wishes the more Debian maintainers are able to enhance their system for their own and their users profit.

In order to achieve a cooperation between virtual organisations, which seems essential since a single Grid has many virtual organisations and the virtual organisations may work across Grids, an infrastructure and policies for their cooperation is required. We regards this as equivalent to the collaboration between individuals, which is exactly what Debian was developed for.

Table 1: Overview on packages in Debian-Med. $^*$ marks packages of collaborators of Debian Med that are not yet part of the Debian main distribution, $^{**}$ marks Debian packages made available through third parties.
Programming libraries: BioPerl, BioPython
Sequence similarity: BLAST2, Cluster3$^*$, ClustalW, e-PCR
Pretty printing: Boxshade, TeXshade$^*$, Textopo$^*$
Phylogeny: Molphy, Phylip, Treeview
Tool collection: EMBOSS$^{**}$, EMBASSY$^{**}$, Bioconductor$^*$, ncbi-tools library and programs, ARB, Primer3$^*$
Molecular modeling: Garlic
Gene detection: Glimmer, Artemis$^{**}$
Genetics: R/qtl
Viewers: Rasmol, Treetool
Pattern discovery: SMILE$^*$, HMMer

Debian harbours the most known and well accepted tools in bioinformatics. An incomplete overview of these is given in table 1. A more detailed overview is available at the Debian-Med website. Debian has means to inform the community of programs that should be packed and the Debian-Med mailing list serves for an additional information transfer.

Andreas Tille 2005-05-13