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Human Genome News Archive Edition

Human Genome News, May 1994; 6(1)

Genome Informatics Minitrack at Hawaii Conference

For the second year, a Genome Informatics Minitrack was included in the Biotechnology Computing Track of the Hawaii International Conference on System Sciences (HICSS). More than 70 biologists, computational biologists, and computer scientists from the United States, Japan, France, and Switzerland attended the 27th meeting, which was held January 4-7 in Maui, Hawaii.

The minitrack was organized by Dong-Guk Shin (University of Connecticut) and Francois Rechenmann (National Institute of Informative and Automatic Research, France). Support was provided jointly by the National Science Foundation, NIH, and DOE. The minitrack included ten rigorously reviewed full papers and four extended abstracts in the following five research subareas of genome informatics.

Data Modeling and Management: modeling biological data and querying; requirements for a high-level database tool; unified way of modeling heterogeneous genomic databases using the Entity-Relationship data model; and adaptability of an interactive query system.

Sequence Analysis: tree data structure and its associated operations that reduce the cost of sequence comparison; approximate string search problem with an external search structure; and method of automating similarity search of expressed sequence tags.

Graphical User Interface: visualizing density and sequence maps; cross-referencing between Genome Data Base (GDB) and GenBank sequence and map links; querying by form-based windows; aligning visually between genetic and sequence maps; supporting a high degree of interface portability; and graphically superimposing GDB locus data on corresponding information from a mouse chromosome.

Interoperation in Heterogeneous Computing Environment: way of making interoperation feasible between two heterogeneous genome databases by using ASN.1 as the common data-exchange language; and strategy that promotes open-system architecture and distributed computing environment for the biology community.

System Integration in Knowledge-Based Approach: method of modeling analysis tasks into knowledge-based objects; software tool designed to automate pre- and post-BLAST search activities using rules elicited from human experts; and deductive object-oriented language to streamline data-retrieval activities.

In addition to the presentation of formal papers, activity reports were presented from the Human Genome Mapping Center at Stanford University by Sidney Cowles and from the Drosophila Genome Center at the University of California, Berkeley, by Suzanna Lewis [Lawrence Berkeley Laboratory (LBL)]. The minitrack also included informal round-table discussion sessions moderated by Shin. Discussion leaders were Mary Berlyn (Yale University), Nathan Goodman (Whitehead Institute-Massachusetts Institute of Technology), Dick Douthart (Pacific Northwest Laboratory), and Manfred Zorn (LBL). Topics discussed in the open forum included standardization for genome database interoperability, relational vs object-oriented modeling of genome data, and use of Mosaic and World Wide Web for data integration across databases.

Plans are being made to include a minitrack on genome informatics at the next HICSS (for details, send an e-mail message to Larry Hunter at hunter@ncbi.nlm.nih.gov).

[Dong-Guk Shin, University of Connecticut]


To request a free copy of the published papers, send e-mail to shin@cse.uconn.edu.

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Human Genome Program, U.S. Department of Energy, Human Genome News (v6n1).

Human Genome Project 1990–2003

The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.

Human Genome News

Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.