Software agents in molecular computational biology
A molecular computational biologist at the United States Meat Animal Research Center (MARC) in Clay Center, Nebraska, part of the Agricultural Research Service within the Department of Agriculture. John leads the bioinformatics efforts at the Center.
Head of computer services at MARC. John and Jim share an interest in applying artificial intelligence and software agents to animal biology.
John W. Keele, United States Meat Animal Research Center, State Spur 18D, Clay Center, Nebraska 68933, USA Tel: +1 402 762 4251 Fax: +1 402 762 4155 E-mail: keele{at}email.marc.usda.gov
Progress made in applying agent systems to molecular computational biology is reviewed and strategies by which to exploit agent technology to greater advantage are investigated. Communities of software agents could play an important role in helping genome scientists design reagents for future research. The advent of genome sequencing in cattle and swine increases the complexity of data analysis required to conduct research in livestock genomics. Databases are always expanding and semantic differences among data are common. Agent platforms have been developed to deal with generic issues such as agent communication, life cycle management and advertisement of services (white and yellow pages). This frees computational biologists from the drudgery of having to re-invent the wheel on these common chores, giving them more time to focus on biology and bioinformatics. Agent platforms that comply with the Foundation for Intelligent Physical Agents (FIPA) standards are able to interoperate. In other words, agents developed on different platforms can communicate and cooperate with one another if domain-specific higher-level communication protocol details are agreed upon between different agent developers. Many software agent platforms are peer-to-peer, which means that even if some of the agents and data repositories are temporarily unavailable, a subset of the goals of the system can still be met. Past use of software agents in bioinformatics indicates that an agent approach should prove fruitful. Examination of current problems in bioinformatics indicates that existing agent platforms should be adaptable to novel situations.
Keywords: software agents, computational biology, bioinformatics, data integrations, artificial intelligence, integration
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  E. Merelli, G. Armano, N. Cannata, F. Corradini, M. d'Inverno, A. Doms, P. Lord, A. Martin, L. Milanesi, S. Moller, et al. Agents in bioinformatics, computational and systems biology Brief Bioinform, January 1, 2007; 8(1): 45 - 59. [Abstract] [Full Text] [PDF]
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