Abstract
We report on the development of an agent-based system, called ΦLOG, for the specification and execution of phylogenetic inference applications. We detail the implementation of the main components of the system. In the process, we discuss how advanced techniques developed in different research areas such as domain-specific languages, planning, Web Services discovery and invocation, and Web Service compositions can be applied in the building of the ΦLOG system.
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References
Entrez, The Life Sciences Search Engine, http://www.ncbi.nlm.nih.gov/Entrez/
European Bioinformatics Institute, http://www.ebi.ac.uk/clustalw/
Gene Data Bank, http://gdbwww.gdb.org/
PDDAML – An Automatic Translator Between PDDL and DAML, www.cs.yale.edu/homes/dvm/daml/pddl_daml_translator1.html
The Bioperl Project, http://www.bioperl.org
UK Human Genome Mapping Project Resource Center, www.hgmp.mrc.ac.uk/MANUAL/
OmniGene: Standardizing Biological Data Interchange Through Web Services (2001), omnigene.sourceforge.net
The BioMOBY Project (2002), http://biomoby.org
Baker, P.G., Brass, A., Bechoofer, S., Goble, C., Paton, N., Stevens, R.: TAMBIS – Transparent Access to Multiple Bioinformatics Information Sources. In: Proceedings of the International Conference on Intelligent Systems for Molecular Biology (1998)
Ball, T. (ed.): Proc. of the 2nd Conference on Domain-specific Languages (2000)
Beavis, R.: The Biopolymer Markup Language (BIOML). TR, ProteoMetrics, LLC (1999)
Cao, S., Qin, L., Wang, W., Zhu, Y., Li, Y.: Application of Gene Ontology in Bio-data Warehouse. In: Stevens, R., McEntire, R. (eds.) 6th Annual Bio-Ontologies Meeting (2003)
Codenie, W., De Hondt, K., Stayaert, P., Vercammen, A.: From custom applications to domain-specific frameworks. Communications of the ACM 40(10), 70–77 (1997)
Consel, C.: Architecturing software using a methodology for language development. In: Palamidessi, C., Meinke, K., Glaser, H. (eds.) ALP 1998 and PLILP 1998. LNCS, vol. 1490, pp. 170–194. Springer, Heidelberg (1998)
Corradini, F., Mariani, L., Merelli, E.: A Programming Environment for Global Activity-based Aplications. In: WOA (2003)
De Giacomo, G., Lespérance, Y., Levesque, H.: ConGolog, a concurrent programming language based on the situation calculus. Artificial Intelligence 121(1-2), 109–169 (2000)
De Giacomo, G., Levesque, H.J., Sardiña, S.: Incremental execution of guarded theories. ACM Transactions on Computational Logic 2(4), 495–525 (2001)
De Giacomo, G., Reiter, R., Soutchanski, M.: Execution monitoring of high-level robot programs. In: KRR 1998, pp. 453–465. Morgan Kaufmann Publishers, San Francisco (1998)
Gupta, G., Pontelli, E.: Specification, Implementation, and Verification of Domain Specific Languages: a Logic Programming-based Approach. In: CL: from LP into the Future. Springer, Heidelberg (2001)
Karp, A.H.: Programming for Parallelism. Computer 20 (May 1987)
Maddison, D.R., Swofford, D.L., Maddison, W.P.: NEXUS: An Extensible File Format for Systematic Information. Syst. Biol. 464(4), 590–621 (1997)
McIlraith, S., Son, T.C.: Adapting golog for composition of semantic web services. In: KR 2002, pp. 482–493. Morgan Kaufmann Publisher, San Francisco (2002)
Pearson, S.: DAS: Open Source System for Exchanging Annotations of Genomic Sequence Data. Technical report, Open Bioinformatics Foundation (2002)
Pontelli, E., Ranjan, D., Gupta, G., Milligan, B.: Design and Implementation of a Domain Specific Language for Phylogenetic Inference. J. Bio. and Comp. Bio. 2(1), 201–230 (2003)
Reiter, R.: KNOWLEDGE IN ACTION: Logical Foundations for Describing and Implementing Dynamical Systems. MIT Press, Cambridge (2001)
Son, T.C., Pontelli, E., Ranjan, D., Milligan, B., Gupta, G.: An Agent-based Domain Specific Framework for Rapid Prototyping of Applications in Evolutionary Biology. In: Leite, J., Omicini, A., Sterling, L., Torroni, P. (eds.) DALT 2003. LNCS (LNAI), vol. 2990, pp. 76–96. Springer, Heidelberg (2004)
Stevens, R.: Bio-Ontology Reference Collection, http://cs.man.ac.uk/~stevens/onto-publications.html
Van Den Brand, M.G.J., Heering, J., Klint, P., Olivier, P.A.: Compiling Language Definitions: the ASF+SDF Compiler. ACM Trans. on Prog. Languages and Systems 24(4) (2002)
Waldinger, R.: Deductive composition of Web software agents. In: Rash, J.L., Rouff, C.A., Truszkowski, W., Gordon, D.F., Hinchey, M.G. (eds.) FAABS 2000. LNCS (LNAI), vol. 1871. Springer, Heidelberg (2001)
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Pan, Y., Tu, P.H., Pontelli, E., Son, T.C. (2005). Construction of an Agent-Based Framework for Evolutionary Biology: A Progress Report. In: Leite, J., Omicini, A., Torroni, P., Yolum, p. (eds) Declarative Agent Languages and Technologies II. DALT 2004. Lecture Notes in Computer Science(), vol 3476. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11493402_6
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DOI: https://doi.org/10.1007/11493402_6
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