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Bioinformatics has, out of necessity, become a key aspect of drug discovery in the genomic revolution, contributing to both target discovery and target validation. The author describes the role that bioinformatics has played and will continue to play in response to the waves of genome-wide data sources that have become available to the industry, including expressed sequence tags, microbial genome sequences, model organism sequences, polymorphisms, gene expression data and proteomics. However, these knowledge sources must be intelligently integrated.

bioTk is a collection of graphical “widgets” and utilities that support application programming in the domain of bioinformatics. It is intended to establish a framework that encourages the development of communicating window-based applications and flexible, non-modal user interaction. The current release to bioTk has domain-specific widgets for chromosome ideogram displays, genome maps, and scrolling sequence windows.

Building upon Definite Clause Grammar (DCG), a number of logic grammar systems have been developed that are well-suited to phenomena in natural language. We have proposed an extension called String Variable Grammar (SVG), specifically tailored to the biological language of DNA. We here rigorously define and characterize this formalism, showing that it specifies a class of languages that properly contains the context-free languages, but is properly contained in the indexed languages. We give a number of mathematical and biological examples, and use an SVG variant to propose a new abstraction of the process of gene expression. A practical implementation called GenLang is described, and some recent results in parsing genes and other high-level features of DNA sequences are summarized.

The beacon logic-based configurator is designed to ensure the correct and complete configuration of large computer systems at the time of order entry. BEACON is based on a semantic network, KNET , implemented in PROLOG. Unlike other configuration expert systems, BEACON uses a declarative, logic-based approach, as opposed to a data-driven production system or hybrid design. Among other virtues, this allows for a completely interactive ordering session which is guaranteed correct with respect to the underlying model, rather than a batch-mode order-correcting system. KNET allows for configuration by individuation of an abstract, generic representation in a manner that is analogous to the instantiation of logical variables in a PROLOG-style proof.

A much-simplified method for the purification of plasma membranes of cultured cells is presented, based upon the attachment of viable cells to nitrocellulose-treated DEAE-Sephadex beads, and their subsequent shearing by hypotonic lysis, agitation on a vortex mixer and sonication. The method is suggested by an older procedure involving attachment to poly-(L-lysine)-coated glass or polyacrylamide beads; the preparation involved in the present method, however, is considerably easier, more rapid and less expensive. Recovery of L-cell plasma membrane marker enzyme activities is approx. 25%, while contamination by internal membrane markers is much less than 1%.