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

  • ️Wed Jan 01 2003

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

Elarbi Badidi et al. BMC Bioinformatics. 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. Please contact the authors for details about setting up a local-network AnaBench site elsewhere.

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Figures

Figure 1
Figure 1

AnaBench architecture. JSP, Java Server pages; ORB, Object Request Broker, the CORBA middleware; GOBASE, Organelle Genome Database [18,19]; PEPdb, Protist EST Program database [20].

Figure 2
Figure 2

AnaBench use-cases. (1) User Registration: provide name, login name, email, and password. (2) User Connection: provide login name and password. (3) Project Management: create new projects, edit or delete an existing project, and list all user's projects. (4) Data Management: add, edit or delete data, and list all data of a project. (5) Tools Management: create, edit, delete, and list analysis categories, applications, and parameters. (6) Analysis: launch analysis applications, display results, and save them in a user's project. (7) Deferred Execution: launch analysis application in deferred mode. (8) Input: select input data for analysis applications from the user's projects. (9) View Results: display analysis results on the user's browser. (10) Save: save analysis results in an existing or in a new project. (11) Protocol Management: create new protocols, edit or delete an existing protocol, and list all user's protocols.

Figure 3
Figure 3

AnaBench CORBA Server objects. Communication between CORBA server objects and biological databases takes place through the JDBC (Java Database Connectivity) API. Communication between JSP pages and CORBA objects is performed through the IIOP (Internet Inter-ORB Protocol) protocol. Java classes are utilities used by JSP pages and include: SessionManagement manages session information; ObjectsReference finds object reference of CORBA objects; JSPGenerator generates JSP screen form from tools description; ResulDeferredThread launches a new thread for a deferred execution of a tool; RemoteBlast sends a BLAST request to the NCBI BLAST server.

Figure 4
Figure 4

Adding a new application to a specific category.

Figure 5
Figure 5

Adding a parameter description (case of the FLIP application)

Figure 6
Figure 6

FLIP JSP screen form.

Figure 7
Figure 7

The graphical tool for the design and execution of pathways.

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