Research interests
My research interests focus on enhancing the information content and usability of biological data delivered by biocomputational software and databases. I am particularly interested in the application of techniques from:
- artificial intelligence: Applications of AI, such as:
- Ontologies for biological data analysis, cf. DIAN (2000) and SMERSH (1999) systems.
- Software agents: DoubleTwist.com agents for automated sequence analysis (1999).
- Neural networks: Artificial neural networks for identifying immunoglobulin sequences.
- Expert systems: Automating cDNA sequence analysis using the CLIPS expert system shell (Surveyor system, 1998).
- visualization: Efficient representation of sequence properties in the Surveyor system (1998).
- cognitive ergonomics: Ease of use and understandability in:
- the MetaCyc.org static pages (2004), a metabolic pathway knowledge base [example]
- the DoubleTwist.com (1999) site, a bioinformatic agent system
- Surveyor (1998), an expert system-based cDNA sequence analysis system
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Selected current projects
- For SRI International's Bioinformatics Research Group: Developing an XML parser for the GenBank database as part of the BioWarehouse project, a component of DARPA's BioSpice project.
- For SRI International's Bioinformatics Research Group: Surveying orphan enzyme activities (enzymes for which no sequence data are available) as part of the Enzyme Genomics Project ("Investigating Unsequenced Enzymatic Activities: A Preliminary to Enzyme Genomics", National Science Foundation).
- For the Monterey Institute of International Studies' Center for Nonproliferation Studies: Developing a database to capture information about the former Soviet Union's anti-plague monitoring system.
- For various units of SRI International: Proposal management for several DARPA and NIH proposals.
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Selected recent projects
- For SRI International's Advanced In Vitro Toxicology Program: Designing and supervising the development of a highly flexible data capture/data management system for biological methods development, based on Oracle, Spotfire and Excel. This system is unique in that it enables biologist users can to what data are captured and how these are treated without the need for software developers and DBAs.
- For SRI International's Bioinformatics Research Group: Re-factoring the MetaCyc database Web site.
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