• Event-Driven Ecological Models
• Good Starting Reading on Petri Nets
• Across Trophic Level System Simulation (ATLSS)
• Neutral Theory and Community Ecology
• More Petri Net Links
• More References

Petri nets have been used in ecological modelling, and appear to have some connection with Ewing’s quantitative population ethology modelling. Carl Adam Petri defined the language, while Kurt Jensen and others have refined and extended. There is a lot of material that COULD be read. May I suggest the following:

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. K�ffner, 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.

Across Trophic Level System Simulation (ATLSS)

The following references are specific to Wolff, another approach to individual-based modelling.

• 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.

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 f�r Petrinetze 1997, Humboldt-Universit�t 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