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Bioinformatics waves at the french Atlantic Coast

Roland's picture

St. Malo: Beautiful location at the west coast of France in Brittany, meeting room just about 50 meter from the seafront, spectacular surroundings in the old town of the city. Pair this with a bunch of bright Debian developers devoted to provide the most extensive and optimally integrated set of open-source Bioinformatics software. By now at the latest it should ring a bell: I'm talking about the DebianMed Sprint 2015.

And it gets even better: For the first time, Qlustar was represented by no less than three developers from Q-Leap Networks. While in general, many technical details about a variety of Bioinformatics packages were discussed at the meeting, work on existing packages progressed and new packages were added, the Q-Leap team also underlined how vital its collaboration with the DebianMed community has become.

In his opening note, DebianMed founder Andreas Tille presented interesting statistics about the project. In the 13 years since its inception, the emphasis put on an extremely open and welcoming spirit in the DebianMed community has led to a tremendous success and an unbelievable number of well-supported packages relevant to medicine and Bioinformatics. I believe, it's no exaggeration, to claim, that this vast collection of integrated software packages is unparalleled in science. Needless to say, that the Qlustar team is very proud, to be a member of this inspiring community.

At my presentation at the sprint, I stressed the importance of the Debian Med project for Qlustar. Our well-defined goal is to provide a state-of-the-art application stack for Bioinformatics software on HPC clusters: The Qlustar BioStack. To achieve this, we port those DebianMed packages, that benefit from running on a cluster to the edge-platforms Qlustar supports at any given time. In essence, the Qlustar BioStack can be viewed as DebianMed optimized for HPC clusters.

In practice, the source of packages to enter Qlustar is always imported from Debian testing. This guarantees a very much up-to-date Bioinformatics software collection based on a stable, well-tested OS base. Furthermore, packages that support MPI are recompiled with Qlustar's optimized version of OpenMPI, thus fully leveraging the compute power of the clusters they run on. A small demo cluster running Qlustar was available for testing in the meeting room.

One particularly pressing issue that was debated at the sprint: The creation of simple-to-use Bioinformatics process pipelines. During his enlightening talk, Tim Booth, creator of BioLinux highlighted the importance of such pipelines in helping researchers to effectively process data from high-throughput sequencing studies. As one of the many concrete steps made forward in St. Malo, Tim and I decided to collaborate on a project, where we target a DebianMed package that will provide a cluster-optimized version of the qiime pipelining tool. Stay tuned.

Another interesting presentation was given by Hervé Ménager on the secrets of Mobyle, a powerful web portal for bioinformatics analysis, that is used at many organizations and jointly developed by the Institut Pasteur Biology IT Center and the Ressource Parisienne en Bioinformatique Structurale. Following that, Luca Clivio reported on security aspects of heavybase, a peer to peer data sharing engine for clinical trials and biobanks. It is in use at a large number of hospitals and developed at the Mario Negri Institute for Pharmacological Research in Milano. Like at previous DebianMed sprints, other important activities were the mentoring for new packagers and the traditional PGP key-signing between project members.

After enjoying a fun Q-Leap sponsored Pizza dinner on Saturday evening, we packed up late Sunday afternoon to hit the road for the less-fun-part of this weekend: The 1000km drive back home. Fortunately the strong snow fall only set in about 100km before Stuttgart. Nevertheless, it was 4:30am, when I switched off the lights, trying to catch at least a little sleep before heading to the UKHPC summit in London the same morning.

Conclusion: This meeting was worth any minute and effort everybody put into it. For us in particular, it was another milestone on the path to make Qlustar a turn-key Bioinformatics cluster stack. Special thanks go to Olivier Sallou, who did a superb job in organizing the event and to Steffen Möller for his continuing dedication in helping to achieve an optimal integration of Qlustar and DebianMed.

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