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      Mobyle: a new full web bioinformatics framework

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          Abstract

          Motivation: For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally, given that scientific tools can be difficult to install, it is particularly helpful for biologists to be able to use these tools through a web user interface. However, providing a web interface for a set of tools raises the problem that a single web portal cannot offer all the existing and possible services: it is the user, again, who has to cope with data copy among a number of different services. A framework enabling portal administrators to build a network of cooperating services would therefore clearly be beneficial.

          Results: We have designed a system, Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software. While being focused on the end user, the Mobyle system also addresses the need, for the bioinfomatician, to automate remote services execution: PlayMOBY is a companion tool that automates the publication of BioMOBY web services, using Mobyle program definitions.

          Availability: The Mobyle system is distributed under the terms of the GNU GPLv2 on the project web site ( http://bioweb2.pasteur.fr/projects/mobyle/). It is already deployed on three servers: http://mobyle.pasteur.fr, http://mobyle.rpbs.univ-paris-diderot.fr and http://lipm-bioinfo.toulouse.inra.fr/Mobyle. The PlayMOBY companion is distributed under the terms of the CeCILL license, and is available at http://lipm-bioinfo.toulouse.inra.fr/biomoby/PlayMOBY/.

          Contact: mobyle-support@ 123456pasteur.fr ; mobyle-support@ 123456rpbs.univ-paris-diderot.fr ; letondal@ 123456pasteur.fr

          Supplementary information: Supplementary data are available at Bioinformatics online.

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          Most cited references 31

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          Usability engineering

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            Direct Manipulation: A Step Beyond Programming Languages

             Shneiderman (1983)
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              The Biology Workbench--a seamless database and analysis environment for the biologist.

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                Author and article information

                Journal
                Bioinformatics
                bioinformatics
                bioinfo
                Bioinformatics
                Oxford University Press
                1367-4803
                1367-4811
                15 November 2009
                17 August 2009
                17 August 2009
                : 25
                : 22
                : 3005-3011
                Affiliations
                1Groupe Logiciels et Banques de Données, Institut Pasteur, 28, rue du Dr Roux, 75724 Paris Cedex, 2UMR-S 936, RPBS, Université Paris Diderot-Paris7, 75205 Paris Cedex 13, 3Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441/2594, INRA/CNRS F-31320 Castanet Tolosan and 4UMR-S 973, RPBS, Université Paris Diderot-Paris7, 75205 Paris Cedex 13, France
                Author notes
                *To whom correspondence should be addressed.

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

                Associate Editor: Alfonso Valencia

                Article
                btp493
                10.1093/bioinformatics/btp493
                2773253
                19689959

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Categories
                Original Papers
                Databases and Ontologies

                Bioinformatics & Computational biology

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