ABSTRACT
The use of complex system simulation as a research tool is facilitated by principled development; software quality assurance, an important part of fitness for purpose, can be assisted by use of model driven engineering (MDE) techniques. The paper addresses two key aspects of MDE for simulation development: the choice of appropriate modelling languages, and language adaptation, illustrated from a cell division and differentiation simulation development, for use in research on prostate conditions. The resulting language has potential for general modelling of reactive and transitional systems.
- P. S. Andrews, F. A. C. Polack, A. T. Sampson, S. Stepney, and J. Timmis. The CoSMoS Process, version 0.1. Technical report, Dept of Computer Science, Univ. of York, 2010. www.cs.york.ac.uk/ftpdir/reports/2010/YCS/453/YCS-2010-453.pdf.Google Scholar
- H. Bersini. UML for ABM. Journal of Artificial Societies and Social Simulation, 15(1):9, 2012.Google ScholarCross Ref
- A. Droop, P. Garnett, F. A. C. Polack, and S. Stepney. Multiple model simulation: modelling cell division and differentiation in the prostate. In CoSMoS Workshop, pages 79--112. Luniver Press, 2011.Google Scholar
- A. J. Flügge, J. Timmis, P. Andrews, J. Moore, and P. Kaye. Modelling and simulation of granuloma formation in visceral Leishmaniasis. In CEC, pages 3052--3059. IEEE Press, 2009. Google ScholarDigital Library
- T. Ghetiu, F. A. C. Polack, and J. Bown. Argument driven validation of computer simulations --- a necessity rather than an option. In VALID, pages 1--4. IEEE, 2010. Google ScholarDigital Library
- M. Heiner and D. Gilbert. How might Petri nets enhance your systems biology toolkit. In Petri Nets, volume 6709 of LNCS, pages 17--37. Springer, 2011. Google Scholar
- L. Hillah, F. Kordon, L. Petrucci, and N. Trèves. Building an API for ISO/IEC 15909, based on model engineering techniques. Technical report, MeFoSyLoMa, 2005. www.mefosyloma.fr/pdf/ISO-IEC-15909/pnNewsLetter6.pdf.Google Scholar
- L. M. Hillah, E. Kindler, F. Kordon, L. Petrucci, and N. Trèves. The Petri Net Markup Language and ISO/IEC 15909-2. In Practical Use of Coloured Petri Nets and the CPN Tools. Aarhus University, 2009. http://cs.au.dk/cpnets/workshops/2009/.Google Scholar
- L.-M. Hillah, F. Kordon, L. Petrucci, and N. Trèves. PNML framework: An extendable reference implementation of the Petri Net Markup Language. In Petri Nets, volume 6128 of LNCS, pages 318--327. Springer, 2010. Google Scholar
- Software and Systems Engineering --- High-level Petri Nets Part 2: Transfer Format. International Standard ISO/IEC 15909, 2005. WD 15909-2:2005(E): www.petrinets.info/docs/ISO-IEC15909-2.WD.V0.9.0.pdf.Google Scholar
- T. Katsube, Y. Yano, T. Wajima, Y. Yamano, and M. Takano. Pharmacokinetic/pharmacodynamic modeling and simulation to determine effective dosage regimens for doripenem. Journal of Pharmaceutical Sciences, 99(5):2483--91, 2010.Google ScholarCross Ref
- H. Kitano, A. Funahashi, Y. Matsuoka, and K. Oda. Using process diagrams for the graphical representation of biological networks. Nature Biotechnology, 23(8):961--6, 2005.Google ScholarCross Ref
- K. W. Kohn and M. I. Aladjem. Circuit diagrams for biological networks. Molecular Systems Biology, 2, 2006. online: doi: 10.1038/msb4100044.Google Scholar
- D. S. Kolovos, L. M. Rose, N. D. Matragkas, R. F. Paige, F. A. C. Polack, and K. J. Fernandes. Constructing and navigating non-invasive model decorations. In ICMT, volume 6142 of LNCS, pages 138--152. Springer, 2010. Google Scholar
- C. Y. Laporte, M. Doucet, P. Bourque1, and Y. Belkébir. Utilization of a set of software engineering roles for a multinational organization. In PROFES, volume 4589 of LNCS. Springer, 2007. Google ScholarDigital Library
- F. A. C. Polack, P. S. Andrews, T. Ghetiu, M. Read, S. Stepney, J. Timmis, and A. T. Sampson. Reflections on the simulation of complex systems for science. In ICECCS, pages 276--285. IEEE Press, 2010. Google ScholarDigital Library
- F. A. C. Polack, A. Droop, P. Garnett, T. Ghetiu, and S. Stepney. Simulation validation: exploring the suitability of a simulation of cell division and differentiation in the prostate. In CoSMoS Workshop, pages 113--133. Luniver Press, 2011.Google Scholar
- M. Read, P. S. Andrews, J. Timmis, and V. Kumar. A domain model of Experimental Autoimmune Encephalomyelitis. In CoSMoS Workshop, pages 9--44. Luniver Press, 2009.Google Scholar
- M. Read, P. S. Andrews, J. Timmis, and V. Kumar. Using UML to model EAE and its regulatory network. In ICARIS, volume 5666 of LNCS. Springer, 2009. Google ScholarDigital Library
Index Terms
- Choosing and adapting design notations in the principled development of complex systems simulations for research
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