Abstract
The dynamic nature of biological systems’ structure, and the continuous evolution of their components require new modelling approaches. In this paper it will be investigated how these systems composed of many dynamic components can be formally modelled as well as how their configurations can be altered, thus affecting the communication between parts. We use two different formal methods, communicating X-machines and population P systems, both with dynamic structures. It will be shown that new modelling approaches are required in order to capture the complex and dynamic nature of these systems.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 226, 1021–1024 (1994)
Banatre, J.P., Le Metayer, D.: The gamma model and its discipline of programming. Science of Computer Programming 15, 55–77 (1990)
Bernardini, F., Gheorghe, M.: Population P Systems. Journal of Universal Computer Science 10, 509–539 (2004)
Bianco, L., Fontana, F., Franco, G., Manca, V.: P systems in Bio Systems. In: Păun, G. (ed.) Application of P systems (2004) (submitted)
Clarke, J., Langton, P., Lu, L., Wu, T., Yang, Y.: Computational models of Pharao’s ants using X-machines. Department of Computer Science, University of Sheffield, MSc final report (2002)
Dorigo, M., Maniezzo, V., Colorni, A.: The Ant System: Optimisation by a colony of co-operating agents. IEEE Transactions on Systems, Man and Cybernetics 26, 1–13 (1996)
Eilenberg, S.: Automata, Languages and Machines. Academic Press, London (1974)
Eleftherakis, G.: Formal Verification of X-Machine Models: Towards Formal Development of Computer-based Systems, PhD Thesis, Department of Computer Science, University of Sheffield (2003)
Eleftherakis, G., Kefalas, P.: Model Checking Safety Critical Systems specified as X-Machines. Analele Universitatii Bucharest, Matematica-Informatica series 49, 59–70 (2000)
Eleftherakis, G., Kefalas, P., Sotiriadou, A.: Formal Modelling and Verification of Reactive Agents for Intelligent Control. In: Proceedings of the 12th Intelligent System Applications to Power Systems Conference, ISAP (2003)
Gregson, A.M., Hart, A.G., Holcombe, M., Ratnieks, F.L.W.: Partial nectar loads as a cause of multiple nectar transfer in the honey bee (Apis mellifera): a simulation model. Journal of Theoretical Biology 222, 1–8 (2003)
Holcombe, M.: X-machines as a Basis for Dynamic System Configuration. Software Engineering Journal 3, 69–76 (1988)
Holcombe, M.: Computational models of cells and tissues: Machines, agents and fungal infection. Briefings in Bioinformatics 2, 271–278 (2001)
Holcombe, M., Ipate, F.: Correct Systems: Building a Business Process Solution. Springer, London (1998)
Ipate, F., Holcombe, M.: An Integration Testing Method that is proved to find all faults. International Journal of Computer Mathematics 63, 159–178 (1997)
Jennings, N.R.: On agent-based software engineering. Artificial Intelligence 117, 277–296 (2000)
Kapeti, E., Kefalas, P.: A Design Language and Tool for X-Machines Specification. In: Fotiadis, D.I., Spyropoulos, S.D. (eds.) Advances in Informatics, pp. 134–145. World Scientific Publishing Company, Singapore (2000)
Kefalas, P.: Automatic translation from X-machines to Prolog. TR-CS01/00, Dept. of Computer Science, CITY Liberal Studies (2000)
Kefalas, P.: XMDL user manual: version 1.6. TR-CS07/00, Dept. of Computer Science, CITY Liberal Studies (2000)
Kefalas, P., Eleftherakis, G., Holcombe, M., Gheorghe, M.: Simulation and Verification of P Systems through Communicating X-Machines. BioSystems 70, 135–148 (2003)
Kefalas, P., Eleftherakis, G., Holcombe, M., Stamatopoulou, I.: Formal Modelling of the Dynamic Behaviour of Biology-Inspired Agent-based Systems. In: Gheorghe, M. (ed.) Molecular Computational Models: Unconventional Approaches. Idea Publishing, Inc, USA (2004) (accepted)
Kefalas, P., Eleftherakis, G., Kehris, E.: Communicating X-Machines: A Practical Approach for Formal and Modular Specification of Large Systems. Journal of Information and Software Technology 45, 269–280 (2003)
Kefalas, P., Eleftherakis, G., Sotiriadou, A.: Developing Tools for Formal Methods. In: Proceedings of the 9th Panhellenic Conference in Informatics, pp. 625–639 (2003)
Martin-Vide, C., Mauri, G., Păun, G., Rozenberg, G., Salomaa, A. (eds.): Membrane Computing, International Workshop, WMC 2003, Tarragona. LNCS, vol. 2933. Springer, Heidelberg (2004) (revised papers)
Păun, G.: Computing with membranes. Journal of Computer and System Sciences 61(1), 108–143 (2000)
Păun, G.: Membrane Computing: An Introduction. Springer, Berlin (2002)
Păun, G., Rozenberg, G., Salomaa, A., Zandron, C. (eds.): Membrane Computing. International Workshop, WMC-CdeA 2002, Curtea de Arges, Romania. LNCS, vol. 2597. Springer, Heidelberg (2002) (revised papers)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Gheorghe, M., Stamatopoulou, I., Holcombe, M., Kefalas, P. (2005). Modelling Dynamically Organised Colonies of Bio-entities. In: Banâtre, JP., Fradet, P., Giavitto, JL., Michel, O. (eds) Unconventional Programming Paradigms. UPP 2004. Lecture Notes in Computer Science, vol 3566. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11527800_17
Download citation
DOI: https://doi.org/10.1007/11527800_17
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-27884-9
Online ISBN: 978-3-540-31482-0
eBook Packages: Computer ScienceComputer Science (R0)