Abstract
Recent years have seen dramatic and sustained growth in the amount of genomic data being generated, including in late 1999 the first complete sequence of a human chromosome. The challenge now faced by biological scientists is to make sense of this vast amount of accumulated and accumulating data. Fortunately, numerous databases are provided as resources containing relevant data, and there are similarly many available programs that analyse this data and attempt to understand it. However, the key problem in analyzing this genomic data is how to integrate the software and primary databases in a flexible and robust way. The wide range of available programs conform to very different input, output and processing requirements, typically with little consideration given to issues of integration, and in many cases with only token efforts made in the direction of usability. In this paper, we introduce the problem domain and describe GeneWeaver, a multi-agent system for genome analysis. We explain the suitability of the information agent paradigm to the problem domain, focus on the problem of incorporating different existing analysis tools, and describe progress to date.
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References
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lippman, D.J.: Basic local alignment search too. Journal of Molecular Biology 215, 403–410 (1990)
Andrade, M.A., Brown, N.P., Leroy, C., Hoersch, S., de Daruvar, A., Reich, C., Franchini, A., Tamames, J., Valencia, A., Ouzounis, C., Sander, C.: Automated genome sequence analysis and annotation. Bioinformatics 15(5), 391–412 (1999)
Bairoch, A., Apweiler, R.: The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Research 27(1), 49–54 (1999)
Barker, W.C., Garavelliand, J.S., McGarvey, P.B., Marzec, C.R., Orcutt, B.C., Srinivasarao, G.Y., Yeh, L.-S.L., Ledley, R.S., Mewes, H.-W., Pfeiffer, F., Tsugita, A., Wu, C.: The PIR-international protein sequence database. Nucleic Acids Research 27(1), 39–43 (1999)
Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer Jr, E.E., Brice, M.D., Rodgers, J.R., Ken-nard, O., Shimanouchi, T., Tasumi, M.: The protein data bank: a computer-based archival file for macromolecular structures. Journal of Molecular Biology 112 (1977)
Bork, P., Koonin, E.V.: Predicting functions from protein sequences: where are the bottlenecks? Nature Genetics 18, 313–318 (1998)
Collins, F.S., Patrinos, A., Jordan, E., Chakravarti, A., Gesteland, R., Walters, L., The members of the DOE and NIH planning groups: New goals for the U.S. human genome project: 1998-2003. Science 282, 682–689 (1998)
Farley, J.: Java Distributed Computing. O’Reilly, Sebastopol (1998)
Foss, J.D.: Brokering the info-underworld. In: Jennings, N.R., Wooldridge, M.J. (eds.) Agent Technology: Foundations, Applications, and Markets, pp. 105–123. Springer, Heidelberg (1998)
Hofmann, K., Bucher, P., Falquet, L., Bairoch, A.: The PROSITE database, its status in 1999. Nucleic Acids Research 27(1), 215–219 (1999)
Jennings, N.R., Wittig, T.: ARCHON: Theory and practice. In: Distributed Artificial Intelligence: Theory and Praxis, pp. 179-195. ECSC, EEC, EAEC (1992)
Jones, D.T.: Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292, 195–202 (1999)
Jones, D.T.: GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. Journal of Molecular Biology 287, 797–815 (1999)
Kuokka, D., Harada, L.: Matchmaking for information agents. In: Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence, pp. 672–679 (1995)
Luck, M., d’Inverno, M.: Engagement and cooperation in motivated agent modelling. In: Zhang, C., Lukose, D. (eds.) DAI 1995. LNCS, vol. 1087, pp. 70–84. Springer, Heidelberg (1996)
Luck, M., d’Inverno, M.: Motivated behaviour for goal adoption. In: Zhang, C., Lukose, D. (eds.) DAI 1998. LNCS (LNAI), vol. 1544, pp. 58–73. Springer, Heidelberg (1998)
Mayfield, J., Labrou, Y., Finin, T.: Evaluating KQML as an agent communication language. In: Tambe, M., Müller, J., Wooldridge, M.J. (eds.) IJCAI-WS 1995 and ATAL 1995. LNCS(LNAI), vol. 1037, pp. 347–360. Springer, Heidelberg (1996)
Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673–4680 (1994)
Vossen, G.: The CORBA specification for cooperation in heterogeneous information systems. In: Kandzia, P., Klusch, M. (eds.) Cooperative Information Agents, pp. 101–115. Springer, Heidelberg (1997)
Wiederhold, G.: Mediators in the architecture of future information systems, vol. 25(3). IEEE Computer, Los Alamitos (1992)
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Bryson, K., Luck, M., Joy, M., Jones, D.T. (2000). Applying Agents to Bioinformatics in GeneWeaver. In: Klusch, M., Kerschberg, L. (eds) Cooperative Information Agents IV - The Future of Information Agents in Cyberspace. CIA 2000. Lecture Notes in Computer Science(), vol 1860. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-45012-2_7
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DOI: https://doi.org/10.1007/978-3-540-45012-2_7
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