This article is part of the supplement: Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010

Open Access Proceedings

Community-driven computational biology with Debian Linux

Steffen Möller12*, Hajo Nils Krabbenhöft23, Andreas Tille2, David Paleino24, Alan Williams5, Katy Wolstencroft5, Carole Goble5, Richard Holland6, Dominique Belhachemi27 and Charles Plessy28

Author Affiliations

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

2 Debian Linux

3 Spratpix, Am Kiel-Kanal 2, 24106 Kiel, Germany

4 Università degli Studi di Palermo, Dipartimento di Scienze Stomatologiche, Via del Vespro 129, 90127 Palermo, Italy

5 University of Manchester, Oxford Road, Manchester,M13 9PL, UK

6 Eagle Genomics, Babraham Research Campus, Cambridge CB22 3AT, UK

7 Section of Biomedical Image Analysis, Department of Radiology, University of Pennsylvania, 3600 Market Street, Suite 360, Philadelphia, PA 19104, USA

8 RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan

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BMC Bioinformatics 2010, 11(Suppl 12):S5  doi:10.1186/1471-2105-11-S12-S5

Published: 21 December 2010

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.