Dear all, over the last weekend in January the Debian Med team hosted the first Sprint on Bioinformatics [1] in Travemünde at the Baltic Sea in Germany. It was an intense time of up to 6 Debian developers (tille, moeller, banck, manuel, cts, schuldei), another two with bioinformatics packages already in the distribution, a representative from Ubuntu derived Bio-Linux [2], another from Knoppix derived Goebix [3] and then all the bioinformatics researchers, teachers and sysadmins that totaled to 25 individuals from 6 countries. The meeting had a couple of very tangible outcomes * The packaging of Ensembl [4] (joint project by the EMBL - EBI and the Wellcome Trust Sanger Institute to produces and maintains automatic annotation on selected genomes) was continued and uploaded to the new queue for experimental. It is prepared by and maintained with all insights from the company Eagle Genomics [5] in Cambridgeshire. They benefit from it themselves when setting up their cloud environments with Debian and so shall everyone else. * New packages - Bowtie - TMalign - rq - vienna-rna - mothur * Revisions in collaboration with upstream - T-Coffee, stimulating the packaging of many additional alignment tools * We got cran2deb [6,7] installed on master.dermacloud.uni-luebeck.de/cran2deb/rep and ran through the 2565 most-easy-to-pack packages from CRAN [8] and another 898 from BioConductor [9] over the last two weeks. * Taverna [10] could already talk to Debian's command line before, but now it can also understand the description of tools in EMBOSS [11] in an automated manner. This involved our community and the representatives from both upstreams alike. But we have met for the soft sides more, where we have to report on * Training on packaging software for Debian on 6 individuals. But as usual, on some higher level everyone learned something from everyone else. Key signing. Hey, quite some of us where seeing each other for the first time. This helps. * We learned about how Debian Med is perceived. There should be less geeky web pages or those that we have be made more obvious. We are doing many things right, but we should advertise them more. We were not completely confident that we have a critical mass of developers already. But we can definitely say that as community Debian Med has long exceeded any regular academic funding scheme. * Discussion of differences and complementary ideas between getData [12] (low tech and close to Debian) and biomaj [13] (very user friendly but no direct interaction with Debian packages) for the automated retrieval of biological data and its post processing. * EMBOSS and BioLib [14] found the right level of abstraction to get linked up. * Bio-Linux and Debian Med have found ways to collaborate (and have done so with T-Coffee and TMalign already). This will be particularly interesting since Bio-Linux is allowing itself not to completely adhere to the DFSG when this helps packages to be used by their community. We have decided to mutually learn from our experiences here and communicate the problems or successes with repackaged software. This mostly addresses e.g. Java programs in the bioinformatics community which frequently depend on a very particular version of a library, and even more often the exact version of a particular Jar is not even known. Bio-Linux can in those cases ship a binary package. We from Debian Med cannot upload binary only packages to main and we do not want to use non-free in this case, even though we could. It would be in our interest to explain Bio-Linux as an extension from what Debian Med is offering. We will be formulating something together in this respect over the next days. * We are still discussing the effect that non-redistributable software (you can download binaries only from the developers but are not allowed to give that to someone else) but with inspect- and buildable sources (you are asked to send patches in) should have on the Debian Med repository. The situation is a bit like the opposite to having only binary packages in Bio-Linux. In the subversion and git repositories of Debian Med we can exchange the code that is required to prepare Debian packages for such software. The source code or the binaries themselves are not shared. Some such software is rather delicate to build and the formalities of the build process to be exchange publicly through us should play well into the hands of the respective communities. The NERC Environmental Bioinformatics Centre in Oxford [15] that is behind Bio-Linux has direcly paid for the travel of multiple participants for ~1000 pounds. This was very generous and we very much thank Tim and the Bio-Linux team for this. We should also consider that as an indication of the special commitment that the Bio-Linux group is preparing for. The employers of the other participants have funded the others' respective travel. Many thanks also go to them. The DDs either came from the region or shall have their costs compensated by Debian funds, which then shall remain well in the budget forseen for the 5-7 people originally planned for. Many thanks to all the participants for a tantalising time together, in the name of all of us Steffen and Andreas [1] http://wiki.debian.org/DebianMed/Meeting/Luebeck2011 [2] http://nebc.nerc.ac.uk/tools/bio-linux/ [3] http://www.bioinf.med.uni-goettingen.de/teaching/goebixdvd [4] http://www.ensembl.org [5] http://www.eaglegenomics.com [6] http://debian.cran.r-project.org [7] http://master.dermacloud.uni-luebeck.de/cran2deb [8] http://cran.r-project.org [9] http://www.bioconductor.org [10] http://www.taverna.org.uk [11] http://emboss.sourceforge.net [12] http://wiki.debian.org/getData [13] http://genome.jouy.inra.fr/biomaj [14] http://biolib.open-bio.org/wiki/Main_Page [15] http://nebc.nerc.ac.uk/
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