Abstract
BackgroundSequence 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.ResultsIn 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.ConclusionAnaBench 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: . Please contact the authors for details about setting up a local-network AnaBench site elsewhere.
Highlights
Sequence data analyses such as gene identification, structure modeling or phylogenetic tree inference involve a variety of bioinformatics software tools
FLIP [1]), identification of ORFs that correspond to conserved proteins by similarity search, retrieval of protein sequences from GenBank using ENTREZ [3], multiple protein alignment, extraction of well aligned sequence stretches, as well as tree inferences and testing
Our goal was to build a Web-based workbench bioinformatics infrastructure, which fulfills the following requirements: For the user: 1) Access to the workbench by employing only a Web browser without the need to download and configure software on his/her computer; 2) Access to individual user workspace on our central servers to save biological data and analysis results, and organization of this workspace in terms of projects; Web-based environments Bioinformatics tools are accessible through Web interfaces using HTML and various scripting languages (CGI, Perl, etc.)
Summary
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. Introduction To conduct sequence analysis, biologists use a variety of bioinformatics software in a sequential fashion. The output of one tool cannot be used as an input for another, without data format conversion. As bioinformatics tools are written in various programming languages and for different operating systems, installation, configuration, and maintenance of these numerous software components is time consuming, costly and requires IT expertise
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