Community-driven computational biology with Debian Linux

Steffen Möller, Hajo N. Krabbenhöft, Andreas Tille, David Paleino, Alan Williams, Katy Wolstencroft, Carole Goble, Richard Holland, Dominique Belhachemi, Charles Plessy

    Research output: Contribution to journalArticlepeer-review


    Background: The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments.Results: The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software.Conclusions: Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers. © 2010 Möller et al; licensee BioMed Central Ltd.
    Original languageEnglish
    Article numberS5
    JournalBMC Bioinformatics
    Issue number12
    Publication statusPublished - 21 Dec 2010

    Research Beacons, Institutes and Platforms

    • Manchester Institute of Biotechnology


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