What is new for Debian Med in Lenny?

February 15th, 2009

We are proud to announce the first release of Debian Med together with Lenny, the new stable version of the Debian operating system.

The Debian Med project continues its healthy growth, which is reflected in a continuous increase of packages for medical care and an increasing number of people 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 new dynamic web pages to present the development status of our project.

The so called task pages 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 task pages 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.

In addition to the user oriented tasks pages we also generate pages which show the bugs concerning the medical software inside Debian. The bugs pages are a useful tool for Debian Med developers to see immediately which packages need to be worked on.

Medical imaging

Many new packages were made for programs supporting the DICOM and Nifti formats, that are important standards in the field of medical imaging: Aeskulap, AMIDE, dinifti, FSLview, ImageJ, PyNIfTi. Thanks to a patch allowing the use of MySQL 5, we could continue to distribute CTN in Lenny. CTSIM, 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 backport.

You can find all the programs for medical imaging in our med-imaging package.

Sequence analysis and bioinformatics

This release saw the arrival in Debian of EMBOSS, a very comprehensive suite of software for sequence analysis, with one of its web interfaces, EMBOSS Explorer, that you can use locally, on your intranet or on the Internet after an installation as simple as typing aptitude install emboss-explorer.

Debian Med now distributes all the major free programs for multiple sequence alignment. One of them, T-Coffee, can function as a meta-aligner (M-Coffee), 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, DM-Coffee, in which Clustal W is substituted by Kalign.

This first release of Debian Med addresses some very medical field of structural bioinformatics. The AutoDock 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 structural packages that are provided by the Debian Science community like Gromacs or PyMol.

You can find all the programs for sequence analysis and bioinformatics in our med-bio package.

Diversification of the medical packages.

Debian Med covers a broad area relevant to medicine, with for instance software for helping people to take care of their health and body (Pondus), software to study the spread of epidemic diseases (Epigrass), and programs for organizing the professional work of medical doctors (GNUMed). The GNUMed server 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.

You can find all the programs for health and medicine in our med-practice, med-epi, and med-tools packages.