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Open Access Research article

AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis

Elarbi Badidi*, Cristina De Sousa, B Franz Lang and Gertraud Burger

Author Affiliations

The Canadian Institute for Advanced Research, Program in Evolutionary Biology. Département de Biochimie, Université de Montréal, 2900, Boul. Édouard Montpetit, Montréal, QC H3T 1J4, Canada

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BMC Bioinformatics 2003, 4:63  doi:10.1186/1471-2105-4-63

Published: 16 December 2003

Abstract

Background

Sequence data analyses such as gene identification, structure modeling or phylogenetic tree inference involve a variety of bioinformatics software tools. Due to the heterogeneity of bioinformatics tools in usage and data requirements, scientists spend much effort on technical issues including data format, storage and management of input and output, and memorization of numerous parameters and multi-step analysis procedures.

Results

In this paper, we present the design and implementation of AnaBench, an interactive, Web-based bioinformatics Analysis workBench allowing streamlined data analysis. Our philosophy was to minimize the technical effort not only for the scientist who uses this environment to analyze data, but also for the administrator who manages and maintains the workbench. With new bioinformatics tools published daily, AnaBench permits easy incorporation of additional tools. This flexibility is achieved by employing a three-tier distributed architecture and recent technologies including CORBA middleware, Java, JDBC, and JSP. A CORBA server permits transparent access to a workbench management database, which stores information about the users, their data, as well as the description of all bioinformatics applications that can be launched from the workbench.

Conclusion

AnaBench is an efficient and intuitive interactive bioinformatics environment, which offers scientists application-driven, data-driven and protocol-driven analysis approaches. The prototype of AnaBench, managed by a team at the Université de Montréal, is accessible on-line at: http://malawimonas.bcm.umontreal.ca:8091/anabench webcite. Please contact the authors for details about setting up a local-network AnaBench site elsewhere.