Community-driven computational biology with Debian Linux

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 sharin...

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Veröffentlicht in:	BMC bioinformatics Jg. 11; H. Suppl 12; S. S5
Hauptverfasser:	Möller, Steffen, Krabbenhöft, Hajo Nils, Tille, Andreas, Paleino, David, Williams, Alan, Wolstencroft, Katy, Goble, Carole, Holland, Richard, Belhachemi, Dominique, Plessy, Charles
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	London BioMed Central 21.12.2010 Springer Nature B.V
Schlagworte:	Algorithms Bioinformatics Biomedical and Life Sciences Computational Biology - methods Computational Biology/Bioinformatics Computer Appl. in Life Sciences Infrastructure Internet Life Sciences Microarrays Proceedings Software Command Line Remote Machine Cloud Computing Heterogeneous Computing Environment Open Source Movement
ISSN:	1471-2105, 1471-2105
Online-Zugang:	Volltext
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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.
AbstractList	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. 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. 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. 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. 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.BACKGROUNDThe 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.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.RESULTSThe 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.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.CONCLUSIONSDebian 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. 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. 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. 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. 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.
ArticleNumber	S5
Author	Plessy, Charles Paleino, David Möller, Steffen Williams, Alan Goble, Carole Tille, Andreas Wolstencroft, Katy Krabbenhöft, Hajo Nils Holland, Richard Belhachemi, Dominique
AuthorAffiliation	5 University of Manchester, Oxford Road, Manchester,M13 9PL, UK 2 Debian Linux 3 Spratpix, Am Kiel-Kanal 2, 24106 Kiel, Germany 6 Eagle Genomics, Babraham Research Campus, Cambridge CB22 3AT, UK 4 Università degli Studi di Palermo, Dipartimento di Scienze Stomatologiche, Via del Vespro 129, 90127 Palermo, Italy 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 1 University Clinics of Schleswig-Holstein, Department of Dermatology, formerly University of Lübeck, Institute for Neuro- andBioinformatics, Ratzeburger Allee 160, 23530 Lübeck. Germany
AuthorAffiliation_xml	– name: 4 Università degli Studi di Palermo, Dipartimento di Scienze Stomatologiche, Via del Vespro 129, 90127 Palermo, Italy – name: 6 Eagle Genomics, Babraham Research Campus, Cambridge CB22 3AT, UK – name: 3 Spratpix, Am Kiel-Kanal 2, 24106 Kiel, Germany – name: 5 University of Manchester, Oxford Road, Manchester,M13 9PL, UK – name: 7 Section of Biomedical Image Analysis, Department of Radiology, University of Pennsylvania, 3600 Market Street, Suite 360, Philadelphia, PA 19104, USA – name: 8 RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan – name: 2 Debian Linux – name: 1 University Clinics of Schleswig-Holstein, Department of Dermatology, formerly University of Lübeck, Institute for Neuro- andBioinformatics, Ratzeburger Allee 160, 23530 Lübeck. Germany
Author_xml	– sequence: 1 givenname: Steffen surname: Möller fullname: Möller, Steffen email: moeller@debian.org organization: Department of Dermatology, formerly University of Lübeck, Institute for Neuro- andBioinformatics, University Clinics of Schleswig-Holstein, Debian Linux – sequence: 2 givenname: Hajo Nils surname: Krabbenhöft fullname: Krabbenhöft, Hajo Nils organization: Debian Linux, Spratpix – sequence: 3 givenname: Andreas surname: Tille fullname: Tille, Andreas organization: Debian Linux – sequence: 4 givenname: David surname: Paleino fullname: Paleino, David organization: Debian Linux, Dipartimento di Scienze Stomatologiche, Università degli Studi di Palermo – sequence: 5 givenname: Alan surname: Williams fullname: Williams, Alan organization: University of Manchester – sequence: 6 givenname: Katy surname: Wolstencroft fullname: Wolstencroft, Katy organization: University of Manchester – sequence: 7 givenname: Carole surname: Goble fullname: Goble, Carole organization: University of Manchester – sequence: 8 givenname: Richard surname: Holland fullname: Holland, Richard organization: Eagle Genomics – sequence: 9 givenname: Dominique surname: Belhachemi fullname: Belhachemi, Dominique organization: Debian Linux, Section of Biomedical Image Analysis, Department of Radiology, University of Pennsylvania – sequence: 10 givenname: Charles surname: Plessy fullname: Plessy, Charles organization: Debian Linux, RIKEN Omics Science Center
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/21210984$$D View this record in MEDLINE/PubMed
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Copyright	Möller et al; licensee BioMed Central Ltd. 2010 2010 Möller et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Copyright ©2010 Möller et al; licensee BioMed Central Ltd. 2010 Möller et al; licensee BioMed Central Ltd.
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Keywords	Command Line Remote Machine Cloud Computing Heterogeneous Computing Environment Open Source Movement
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Snippet	Background The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources... The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for... Abstract Background: The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and...
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Title	Community-driven computational biology with Debian Linux
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