Mobyle: a new full web bioinformatics framework


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 ( It is already deployed on three servers:, and The PlayMOBY companion is distributed under the terms of the CeCILL license, and is available at

DOI: 10.1093/bioinformatics/btp493

Extracted Key Phrases

4 Figures and Tables

Showing 1-10 of 31 references

Participatory design of pipeline tools and web services in bioinformatics

  • C Letondal, O Amanatian
  • 2004
Highly Influential
2 Excerpts

Soaplab -a unified sesame door to analysis tools

  • M Senger
  • 2003
Highly Influential
3 Excerpts

BioWorkFlow: web services toolkit and workflow applications evaluation to deploy a confidence network

  • M Wessner
  • 2008

Biocatalogue: a curated web service registry for the life science community

  • K Belhajjame
  • 2008
Showing 1-10 of 85 extracted citations
Citations per Year

340 Citations

Semantic Scholar estimates that this publication has received between 201 and 543 citations based on the available data.

See our FAQ for additional information.