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

Community-driven computational biology with Debian Linux

Steffen Möller  1 , Hajo Nils Krabbenhöft, Andreas Tille, David Paleino, Alan Williams, Katy Wolstencroft, Carole Goble, Richard Holland, Dominique Belhachemi, Charles Plessy
Affiliations

Community-driven computational biology with Debian Linux

Steffen Möller et al. BMC Bioinformatics. .

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.

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Figures

Figure 1
Figure 1
This graphical representation of a workflow in Taverna was taken directly from workflow 377 at the myExperiment site. It requests two PDB IDs to retrieve the respective protein structure and present it to the mustang protein structure alignment tool. Its result files are directly offered also as outputs of the workflow. It is only one alignment that is passed throught the tool boxshade for pretty-printing.
See this image and copyright information in PMC

References

    1. Cochrane GR, Galperin MY. The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. Nucleic Acids Res. 2010;38:D1–D4. doi: 10.1093/nar/gkp1077. - DOI - PMC - PubMed
    1. Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T. Taverna: a tool for building and running workflows of services. Nucleic Acids Res. 2006;34(Web Server issue):W279–W232. doi: 10.1186/1471-2105-9-334. http://www.taverna.org.uk/ - DOI - PMC - PubMed
    1. Goble CA, Baghat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, Borkum M, Bechhofer S, Roos M, Li P, De Roure D. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Res. 2010;38:W677–W682. doi: 10.1093/nar/gkq429. - DOI - PMC - PubMed
    1. Debian – the Universal Operating System. http://www.debian.org/
    1. Krabbenhöft H, Möller S. Integrating ARC grid middleware with Taverna workflows. Bioinformatics. 2008;24:1221–1222. doi: 10.1093/bioinformatics/btn095. - DOI - PubMed

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