Abstract
Immune system is complex system which is composed of thousands entities interacting with each other. If we want to understand the immune system behavior, we can use the bottom-up approach investigating interactions occurring in the low-levels (e. g. molecular level) where particular biological entities exist. Multi-agent systems are bottom-up approach used for exploration of the immunity, but the complexity complicates clarifying immune processes. The paper investigates the Agent Modeling Language (AML) for conceptual modeling of particular immune properties and processes. T-cell dependent B-cell activation is used as the case study for finding out if the language can offer value added for conceptual modeling in computational immunology.
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References
Petri, C.A.: Kommunikation mit Automaten, Dissertation Thesis, Institut für Instrumentelle Mathematik, Schriften des IIM, nr. 2, 68 (1964)
Murphy, K.: Janeway´s Immunobiology. Garland Science (2014)
Blätke, M.A.: Tutorial Petri Nets in Systems Biology, http://www.regulationsbiologie.de/pdf/BlaetkeTutorial.pdf
Carvalho, R.V., et al.: Modeling Innate Immune Response to Early Mycobacterium Infection. J. Computational and Mathematical Methods in Medicine (2012), http://www.hindawi.com/journals/cmmm/2012/790482/
Chen, P.: The Entity-Relationship Model - Toward a Unified View of Data. J. ACM Transactions on Database Systems 1, 9–36 (1976)
Bornberg-Bauer, E., Paton, N.W.: Conceptual data modeling for bioinformatics. J. Briefings in Bioinformatics 3, 166–180 (2002)
Harel, D.: Statecharts: A visual formalism for complex systems. J. Science of Computer Programming 8, 231–274 (1987)
Swerdlin, N., Cohen, I.R., Harel, D.: The Lymph Node B Cell Immune Response: Dynamic Analysis In-Silico. In: Proc. of The IEEE, pp. 1421–1442. IEEE Press, New York (2008)
Belkacem, K.: Foudil, Ch.: An Anylogic Agent Based Model for the Lymph Node Lymphocytes First Humoral Immune Response. In: The International Conference on Bioinformatics and Computational Biology, pp. 163–169. IACSIT Press, Singapore (2012)
Kugler, H., Larjo, A., Harel, D.: Biocharts – a visual formalism for modeling biological systems. J. of The Royal Society Interface 7, 1015–1024 (2010), http://research.microsoft.com/pubs/115444/rsif20090457.pdf
Gruber, T.R.: A Translation Approach to Portable Ontology Specification. J. Knowledge Acquisition 5, 199–220 (1993)
Ashburner, M., et al.: Gene Ontology: tool for the unification of biology. J. Nat. Genet. 25, 25–29 (2000)
Hucka, M., et al.: Systems Biology Markup Language (SBML) Level 1 - Structures and Facilities for Basic Model Definitions, http://sbml.org/Special/specifications/sbml-level-1/version-1/sbml-level-1.pdf
Hucka, M., et al.: The Systems Biology Markup Language (SBML): Language Specification for level 3 version 1 Core, http://sbml.org/Special/specifications/sbml-level-3/version-1/core/sbml-level-3-version-1-core.pdf
Bersini, H.: Immune System Modeling: The OO Way. In: Bersini, H., Carneiro, J. (eds.) ICARIS 2006. LNCS, vol. 4163, pp. 150–163. Springer, Heidelberg (2006)
Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N., Kitano, H.: CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. In: Proc. of The IEEE, pp. 1254–1265. IEEE Press, New York (2008)
König, M., Drager, A., Holzhutter, H.-G.: CySBML: a Cytoscape plugin for SBML. J. of Bioinformatics 28, 2402–2403 (2012), http://bioinformatics.oxfordjournals.org/content/early/2012/07/05/bioinformatics.bts432.full.pdf
Le Novère, N., et al.: The Systems Biology Graphical Notation. J. Nature Biotechnology 27, 735–741 (2009)
Flugge, J., Timmis, P., Andrews, J.: Moore and P. Kaye: Modelling and Simulation of Granuloma Formation in Visceral Leishmaniasis. In: Congress on Evolutionary Computation, pp. 3052–3059. IEEE Press, New York (2009)
Read, M., Timmis, J., Andrews, P., Kumar, V.: Domain Model of Experimental Autoimmune Encephalomyelitis. In: Proc. of the 2009 Workshop on Complex Systems Modelling and Simulation, pp. 9–44 (2009)
Červenka, R., Trenčanský, I.: The Agent Modeling Language – AML: A Comprehensive Approach to Modeling Multi-Agent Systems. Springer Science & Business Media, New York (2007)
Abbas, A.K., Lichtman, A., Pillai, S.: Cellular and Molecular Immunology. Saunders, United States (2011)
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Husáková, M. (2015). The Usage of the Agent Modeling Language for Modeling Complexity of the Immune System. In: Barbucha, D., Nguyen, N., Batubara, J. (eds) New Trends in Intelligent Information and Database Systems. Studies in Computational Intelligence, vol 598. Springer, Cham. https://doi.org/10.1007/978-3-319-16211-9_33
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DOI: https://doi.org/10.1007/978-3-319-16211-9_33
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-16210-2
Online ISBN: 978-3-319-16211-9
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