Abstract
For reusing model components, it is crucial to understand what information is needed and how it should be presented. The centrality of abstraction being inherent in the modelling process distinguishes model components from software components and makes their reuse even more difficult. Objectives and assumptions which are often difficult to explicitate become an important aspect in describing model components. Following the argumentation line of the Web Service ontology OWL-S, we propose a set of metadata which is structured into profile, process model, and grounding to describe model components. On the basis of the specific model component Tryptophan Synthase, its metadata is refined in XML. The reuse of the described model component is illustrated by integrating it into a model of the Tryptophan operon.
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Anderson, K.S., Kim, A.Y., Quillen, J.M., Sayers, E., Yand, X.J., Miles, E.W.: Kinetic characterization of channel impaired mutants of tryptophan synthase. The Journal of Biological Chemistry 270(50), 29936–29944 (1995)
Aronson, J., Bose, P.: A model-based approach to simulation composition. In: Proceeding of the Fifth Symposium on Software Reusability, pp. 73–82 (1999)
Barros, F., Sarjoughian, H. (eds.): Special Issue on Component-Based Modelling and Simulation. Simulation – Transactions of the SCS Simulation. Sage, Thousand Oaks (2004)
Biermann, S., Uhrmacher, A.M., Schumann, H.: Supporting multi-level models in systems biology by visual methods. In: Proceedings of European Multi-Simulation Conference (2004) (page submitted)
Buss, A., Jackson, L.: A comparison of hla, corba, and rmi. In: Proceedings of the 1998 Winter Simulation Confrence, pp. 819–825 (1998)
Cellier, F.E.: Continuous System Modeling. Springer, New York (1992)
Chen, G., Szymanski, B.K.: Object-oriented paradigm: component-oriented simulation architecture: toward interoperability and interchangeability. In: Proceedings of the 2001 Winter Simulation Conference, pp. 495–501 (2001)
Chen, G., Szymanski, B.K.: Cost: A component-oriented discrete ecent simulator. In: Proceedings of the 2002 Witer Simulation Conference, pp. 776–782 (2002)
Cuellar, A.A., Lloyed, C.M., Nielsen, P.F., Bullivant, D.P., Nickerson, D.P., Hunter, P.J.: An overview of of cellml 1.1, a biological model description language. Simultation – Transaction of the SCS 79(12), 740–747 (2003)
Dahmann, J., Fujjimoto, R., Weatherly, R.: The dod high level architecture: An update. In: Proceddings of the 1998 Winter Simulation Conference, pp. 797–804 (1998)
Davis, P.K., Bigelow, J.H., McEver, J.: Exploratory analysis and a case history of multi-resolution, multiperspective modeling. Technical Report RP-925, RAND (2000)
de Lara, J., Vangheluwe, H.: AToM3: A tool for multi-formalism and meta-modelling. In: Kutsche, R.-D., Weber, H. (eds.) FASE 2002, vol. 2306, pp. 174–188. Springer, Heidelberg (2002)
Degenring, D., Röhl, M., Uhrmacher, A.M.: Discrete event simulation for a better understanding of metabolite channeling - A system theoretic approach. In: CMSB 2003. LNCS, vol. 2602, pp. 114–126. Springer, Heidelberg (2003)
Fishwick, P.A.: Using xml for simulation modeling. In: Proceedings of the 2002 Winter Simulation Conference (2002)
Gillespie, D.T.: Ageneral method for numerically simulation the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics 22, 403–434 (1976)
Heisel, M., Luethi, J., Uhrmacher, A.M., Valentin, E.: A description structure for simulation model components. In: Proceedings of the Summer Simulation Confrernce (2004) (page submitted)
Hnich, B., Jonsson, T., Kiziltan, Z.: On the definition of concepts in component based software development. Technical report, University Department of Information Science, Uppsala, Sweden (2000)
Kam, N., Harel, D., Kugler, H., Marelly, R., Pnueli, A., Hubbard, E.J., Stern, M.J.: Formal modeling of c.elegans development: A scenario based approach. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 4–20. Springer, Heidelberg (2003)
Kitano, H.: A graphical notation for biochemical networks. Biosilico 1(5), 169–176 (2003)
Klettke, M., Meyer, H.: XML & Datenbanken – Konzepte, Sprachen und Systeme. DPunkt Verlag (2003)
Mackulak, G., Lawrence, F.: Effective simulation model reuse; a case study for amhs modeling. In: Proceedings of the 1998 Winter Simulation Conference, pp. 979–984 (1998)
Marhl, M.: Transaction from stochastic to deterministic behaviour in dependence on the divergence of systems. In: 3rd Workshop on Comutation of Beiochemical Pathways and Genetic Networks, pp. 49–58. Logos Verlag (2003)
Miller, Y., Ge, J.A., Tao, J.: Component –based simulation environments: Jsim as a case study using java beans. In: Proceedings of the 1998 Winter Simulation Conference, pp. 373–381 (1998)
Minsky, M.: Models, Minds, Machines. In: Proc. IFIP Congress, pp. 45–49 (1965)
Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.: Genomic object net: a platform for modeling and simulating biopathways. Applied Bioinformatics (2003)
Overstreet, C.M., Nance, R.M., Balci, O.: Issue in enhancing model reuse. In: First International Conference on Grand Challenges for Modeling and Simulation (2002)
Page, E., Opper, J.: Observations on the complexity of composable simulation. In: Proceddings of the 1999 Winter Simulation Conference, Pages, pp. 553–560 (1999)
Santill’an, M., Mackey, M.C.: Dynamic regulation of the tryptophan operon: A modeling study and comparison with experimental data. In: Proceeding of the National Academy of Science of the USA, vol. 98(4), pp. 1364–1369 (2001)
Uhrmacher, A.M., Tyschler, P., Tyschler, D.: Modeling Mobile Agents. Future Generation Compter System 17, 107–118 (2000)
Valentin, E.C., Verbraeck, A., Sol, H.G.: Effect of simulation building blocks on simulation model development. In: Proceddings of the Internation Conference of Technology, Policy and Innovation, Pages CD-ROM Proceedings (2003)
Vangheluwe, H., de Lara, J.: Meta-models are models too. In: Proc. of the Winter Simulation Conference, pp. 597–605 (2002)
Zeigler, B.P.: Multifacetted Modelling and Discrete Event Simulation. Academic Press, London (1984)
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Uhrmacher, A.M., Degenring, D., Lemcke, J., Krahmer, M. (2005). Towards Reusing Model Components in Systems Biology. In: Danos, V., Schachter, V. (eds) Computational Methods in Systems Biology. CMSB 2004. Lecture Notes in Computer Science(), vol 3082. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-25974-9_15
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DOI: https://doi.org/10.1007/978-3-540-25974-9_15
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