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BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S5. doi: 10.1186/1471-2105-11-S12-S5.

Community-driven computational biology with Debian Linux.

Author information

  • 1University Clinics of Schleswig-Holstein, Department of Dermatology, formerly University of Lübeck, Institute for Neuro- andBioinformatics, Ratzeburger Allee 160, 23530 Lübeck, Germany. moeller@debian.org

Abstract

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.

PMID:
21210984
[PubMed - indexed for MEDLINE]
PMCID:
PMC3040531
Free PMC Article

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