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Bioinformatics Advance Access originally published online on August 17, 2009
Bioinformatics 2009 25(22):3005-3011; doi:10.1093/bioinformatics/btp493
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© The Author(s) 2009. Published by Oxford University Press.
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.

Mobyle: a new full web bioinformatics framework

Bertrand Néron 1,{dagger}, Hervé Ménager 1,{dagger}, Corinne Maufrais 1, Nicolas Joly 1, Julien Maupetit 2, Sébastien Letort 3, Sébastien Carrere 3, Pierre Tuffery 4 and Catherine Letondal 1,*

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

*To whom correspondence should be addressed.


  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{at}pasteur.fr; mobyle-support{at}rpbs.univ-paris-diderot.fr; letondal{at}pasteur.fr

Supplementary information:Supplementary data are available at Bioinformatics online.

{dagger}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

Received on April 17, 2009; revised on July 10, 2009; accepted on July 30, 2009

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