title: AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Département de Biochimie, Université de Montréal, 2900, Boul, Edouard Montpetit, Montréal, QC H3T 1J4, Canada. me.badidi@umontreal.ca
authors.forename: Elarbi
authors.initials: E
authors.lastname: Badidi
authors.forename: Cristina
authors.initials: C
authors.lastname: De Sousa
authors.forename: B Franz
authors.initials: BF
authors.lastname: Lang
authors.forename: Gertraud
authors.initials: G
authors.lastname: Burger
mesh_terms: D019295:Computational Biology / Q000379:methods / Q000639:trends; D003196:Computer Graphics / Q000639:trends; D003628:Database Management Systems / Q000639:trends; D030541:Databases, Genetic / Q000639:trends; D006801:Humans; D020407:Internet; D009696:Nucleic Acids / Q000235:genetics; D010802:Phylogeny; D011381:Programming Languages; D011506:Proteins / Q000235:genetics; D017421:Sequence Analysis / Q000379:methods* / Q000639:trends; D012984:Software; D012985:Software Design; D014584:User-Computer Interface
chemical_list: D009696:Nucleic Acids; D011506:Proteins