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

doi:10.1186/1471-2105-11-S12-S5

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 journal › Article › peer-review

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. © 2010 Möller et al; licensee BioMed Central Ltd.

Original language	English
Article number	S5
Journal	BMC Bioinformatics
Volume	11
Issue number	12
DOIs	https://doi.org/10.1186/1471-2105-11-S12-S5
Publication status	Published - 21 Dec 2010

Research Beacons, Institutes and Platforms

Manchester Institute of Biotechnology

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10.1186/1471-2105-11-S12-S5

http://www.biomedcentral.com/1471-2105/11/S12/S5

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title = "Community-driven computational biology with Debian Linux",

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. {\textcopyright} 2010 M{\"o}ller et al; licensee BioMed Central Ltd.",

author = "Steffen M{\"o}ller and Krabbenh{\"o}ft, {Hajo N.} and Andreas Tille and David Paleino and Alan Williams and Katy Wolstencroft and Carole Goble and Richard Holland and Dominique Belhachemi and Charles Plessy",

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doi = "10.1186/1471-2105-11-S12-S5",

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AU - Möller, Steffen

AU - Krabbenhöft, Hajo N.

AU - Tille, Andreas

AU - Paleino, David

AU - Williams, Alan

AU - Wolstencroft, Katy

AU - Goble, Carole

AU - Holland, Richard

AU - Belhachemi, Dominique

AU - Plessy, Charles

PY - 2010/12/21

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N2 - 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.

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Community-driven computational biology with Debian Linux

Abstract

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