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About the Biology Workbench

Biology Workbench Summary

The Biology Workbench is a computational interface and environment that permits anyone with a Web browser to readily use bioinformatics, for research, teaching, or learning. It consists of a set of scripts that links the user's Browser to a collection of information sources (databases) and application programs.

The scripts are specialized for the interface of each program and information source. Functionally they transform the interface for each object, whether database or application program, into a common Web-based form that permits them to be seamlessly interconnected. The user is then able to compile a customized search-and-analyze computational strategy to answer complicated questions about the contents of the databases. By reducing all the formats to a common point-and-click Web interface, the users are freed from the necessity of knowing details of the object fomats. Also the scripts work through the interfaces very rapidly, so various operations can be done quickly. Reasonable default parameters for the various operations are built into the Web interface. However the knowedgeable user can easily adjust parameters for search and analysis via Web menus.

The present version of the Biology Workbench contains a large array of databases and computational tools that are most useful to the molecular biology community for understanding sequence relationships among proteins and nucleic acids. All databases and computer programs are freely accessible to anybody in the world with a networked computer, via Silicon Graphics servers at the National Center for Supercomputing Applications and the San Diego Supercomputer Center. Reflecting the revolutionary architecture of the Workbench, NCSA and SDSC have taken the revolutionary step of making their supercomputers and the Workbench freely available to all without prior arrangement. The Workbench has been publicly available since June 1996. It has steadily grown in the number of users, and the amount of use. Presently there are approximately 11,000 registered users who use the Workbench for about 150,000 computing sessions a month.

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Education Project Summary

The goal of this project is to promote the use of molecular data in the identification and exporation of biological problems wiht an evolutionary perspective throughout undergraduate biology curricula. This will be accomplished by providing undergraduate faculty and students access to the powerful state-of-the-art bioinformatics tools currently in use by the research community transformed to afford a cognitively supportive environment. These products will enable undergraduate students to investigate current problems in biology using molecular biology tools and skills. The objectives of the project are:

  • create the Biology Student Workbench, an educational front-end to the powerful suite of tools comprising the Biology Workbench for use by undergraduate students and instructors
  • develop, test, evaluate and disseminate supportive inquiry-based curricular materials for diverse areas of biology nationwide, and
  • establish a community of inquiry, with scientists, educators and biology students using advanced science concepts and Workbench tools which will sustain, support and further disseminate the use of research tools within education.

The Biology Workbench ( is widely recognized as a significant bioinformatics resource because it provides a suite of interactive tools which draw on a host of biology databases and allows users to compare molecular sequences using high performance computing facilities, visualize and manipulate molecular structures, and generate phylogenetic hypotheses. The Biology Student Workbench will bring the advanced computational infrastructure used by today's scientists to any student desktop machine with a web browser. This access to a multiplicity of research analysis tools and data sources will provide a rich environment for promoting student inquiry.

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