Petri Nets and Ecological Modelling

Event-Driven Ecological Models

• Donalson DD (2000) Modeling complex interactions: Theoretical ecology meets Pacman. U CA Santa Barbara, 146 pages. [PhD Thesis]
• Donalson DD, Nisbet RM (1999) Population dynamics and spatial scale: effects of system size on population persistence. Ecology 80: 2492-2507. [Paper]
• Renshaw E (1993) Modelling Biological Populations in Space and Time. Cambridge U Press. [Book]
• The Institute for Environmental Modeling, U TN Knoxville
• Ecology, Evolution and Marine Biology, UCSB

Good Starting Reading on Petri Nets

1. Petri Nets Frequently Asked Questions
2. Jensen K (1997) Brief Introduction to Coloured Petri Nets, Third International Workshop on Tools and Algorithms for the Construction and Analysis of Systems. TACAS'97, April 2-4 1997, University of Twente, Enschede, The Netherlands
3. H. Genrich, R. Küffner, K. Voss: Executable Petri Net Models for the Analysis of Metabolic Pathways. In: K. Jensen (ed.): Proceedings of the Workshop on Practical Use of High-level Petri Nets, Aarhus 2000, Department of Computer Science, University of Aarhus, PB-547, 1-14. (just print these pages from 152-page, 2.8Mb proceedings)
4. Coloured Petri Nets Introduction, CP Nets Group, U Aarhus
5. A Gronewold, M Sonnenschein (1998) Event-based modelling of ecological systems with asynchronous cellular automata. Ecological Modelling 108: 37-52.

6. More Petri Net Links & References

Across Trophic Level System Simulation (ATLSS)

• WF Wolff (1994) An individual-based model of a wading bird nesting colony. Ecological Modelling 72: 75-114.
• WF Wolff, PA Fishwick (2001?) Wading Bird Simulation Modeling and Integration into ATLSS Landscape and Fish Models, USGS Project
• PA Fishwick (1996) Extending Object-Oriented Design for Physical Modeling Special Issue on Model Specification & Representation, ACM Trans Model Comp Simul. [draft]
• P Fishwick, B O'Keefe, RE Nance (1995) Special issue on graphics, animation, and visualization for simulation environments. ACM Transactions on Modeling and Computer Simulation (TOMACS) 5(3)
• K Lee, PA Fishwick (1999) OOPM/RT: a multimodeling methodology for real-time simulation. ACM Transactions on Modeling and Computer Simulation 9: 141-170.

Neutral Theory and Community Ecology

• Chave J (2004) Neutral theory and community ecology. Ecol Lett 7: 241-253. [doi:10.1111/j.1461-0248.2003.00566.x]
• Chave J, Norden N (2007) Changes of species diversity in a simulated fragmented neutral landscape. Ecol Model 207: 3-10. [doi:10.1016/j.ecolmodel.2007.03.025]
• Economo EP, Keitt TH (2008) Species diversity in neutral metacommunities: a network approach. Ecol Lett 11: 52-62. [doi:10.1111/j.1461-0248.2007.01126.x]
• Harte J (2003) Ecology: Tail of death and resurrection. Nature 424: 1006-1007. [doi:10.1038/4241006a]
• McGill BJ, Maurer BA, Weiser MD (2006) EMPIRICAL EVALUATION OF NEUTRAL THEORY. Ecology 87: 1411-1423. [doi:10.1890/0012-9658(2006)87[1411:EEONT]2.0.CO;2]

More Petri Net Links

• Petri Nets World
• Design/CPN
• Colored Petri Nets Group, U Aarhus
  • 21st International Conference on Application and Theory of Petri Nets, Aarhus, Denmark, June 26-30, 2000
  • Introductory Tutorial (270 pages, 7Mb)
• Lists of Links from Unige & Mikhail
• Other Courses and Introductions
  • System Architectures for Large Scale Systems, George Mason U (1998)
    • ViewGraphs
  • Introduction to and comparison of formalisms, Finland
  • Course on Petri Nets
• Petri Net Markup Language

More References

• Aghasaryan A et al. (1997) A Petri net approach to fault detection and diagnosis in distributed systems. INRIA. [Paper]
• Ajmone Marsan M, Balbo G, Conte G, Donatelli S, Franceschinis G (1995) Modelling with Generalized Stochastic Petri Nets. John Wiley. QA 276 A66
• Berthomieu B, Diaz M (1991) Modeling and verification of time dependent systems using time Petri nets. IEEE Transactions on Software Engineering 17: 259-273. [Abstract]
• Bobbio A, Puliafito A, Tekel M (2000) A modeling framework to implement preemption policies in non-Markovian SPNs. IEEE Transactions on Software Engineering 26: 36-54. [Paper]
• Bowden FDJ (2000) A brief survey and synthesis of the roles of time in Petri nets. Mathematical and Computer Modelling 31: 55-68.
• Bucci G, Vicario E (1995) Compositional validation of time-critical systems using communicating time Petri nets. IEEE Transactions on Software Engineering 21: 000-000. [Abstract] S IN5 EL24 T SE
• Cassandras CG (1993) Discrete Event Systems, Modeling and Performance Analysis. Aksen Assoc Inc, Boston MA. T57.6 C38
• Donatelli S, Ribaudo M, Hillston J (1995) A comparison of performance evaluation process algebra and generalized stochastic Petri nets. [Paper]
• Ehrig H, Orejas F, Padberg J (1990) Relevance, integration and classification of specification formalisms and formal specification techniques. [Paper]
• Holliday MA, Vernon MK (1987) A generalized timed Petri net model for performance analysis. IEEE Transactions on Software Engineering 13: 1297-1310.
• Jensen K (1996) Coloured Petri nets. Talk] QA 267 J46
• Juan EYT, Tsai JJP, Murata T, Yi Z (2001) Reduction methods for real-time systems using delay time petri nets. IEEE Transactions on Software Engineering 27: 422-448. [Paper]
• Keen and Lakos [Paper]
• Kristensen LM, Christensen S, Jensen K (1998) special section on coloured petri nets: The practitioner's guide to coloured Petri nets. International Journal on Software Tools for Technology Transfer 2: 98-132. [Paper]
• Levis AH (2000) Discrete Event Systems. Course at George Mason U [Course]
• Lindemann C (1994) Stochastic Modeling using DSPNexpress. Verlag, Oldenberg. S P413 EV19 v. 42(213)
• Robert E, Janneck JW, Naedele M (1997) Using an object-oriented Petri net tool for heterogeneous systems design: a case study. Algorithmen und Werkzeuge für Petrinetze 1997, Humboldt-Universität zu Berlin, Berlin, Germany 2-3 October 1997 [Paper]
• Vojnar T (199x) Various kinds of Petri nets in simulation and modelling. [Paper] [Homepage]
• Wagenhals LW, Levis AH (2000) Course of action development and evaluation. 2000 Command and Control Research and Technology Symposium, Naval Postgraduate School, Monterey, CA, June 26-28, 2000 [Paper]