Petri net, Azimuth wiki.
The Petri Nets World, Department of Informatics, University of Hamburg. Active website dedicated to Petri nets.
Petri Net, Wikipedia.
John Baez, Network Theory.
Darren James Wilkinson, Stochastic Modelling for Systems Biology, Taylor & Francis, New York, 2006. Good introduction to stochastic Petri nets, with applications to gene expression and the Lotka-Volterra equations for predator-prey interactions.
Jeremy Gunawardena, Chemical reaction network theory for in-silico biologists.
Martin Feinberg, Lectures on reaction networks.
Peter J. Haas, Stochastic Petri Nets: Modelling, Stability, Simulation, Springer, Berlin, 2002.
John Baez, Jacob Biamonte and Brendan Fong, Network theory II: stochastic Petri nets, chemical reaction networks and Feynman diagrams. Slides giving an overview of these subjects.
John C. Baez and Jacob Biamonte, Quantum techniques for stochastic mechanics, arXiv:1209.3632 [quant-ph]. Text includes treatment from the ground up of Petri nets, both stochastic and deterministic.
Vladimiro Sassone, On the category of Petri net computations, 6th International Conference on Theory and Practice of Software Development, Proceedings of TAPSOFT ‘95_, Lecture Notes in Computer Science 915, Springer, Berlin, pp. 334-348.
Petri net, $n$Lab.
Craciun, Dickenstein, Shiu and Sturmfels, Toric dynamical systems. On the relation between reaction networks on toric varieties.
Leonard Adleman, Manoj Gopalkrishnan, Ming-Deh Huang, Pablo Moisset and Dustin Reishus, On the mathematics of the law of mass action.
S. Vidal et al, Models of Stochastic Gene Expression and Weyl Algebra, Algebraic and Numeric Biology (LNCS, volume 6479) p 76-97 2012
Compartmental models in epidemiology, Wikipedia.
Peter J. E. Goss and Jean Peccoud, Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets, Proc. Natl. Acad. Sci. USA 95 (June 1998), 6750-6755.
Debjyoti Bera, Petri nets for modeling robots.
Monika Heiner, From Petri nets to differential equations: an integrative approach for biochemical network analysis, Brandenburg University of Technology Cottbus, Dept. of CS, May 2005.
Gang Wang, Ying Zhang, Simon J. Shepherd, Clive B. Beggs, Nini Rao, Application of stochastic Petri nets for modelling the transmission of airborne Infection in Indoor Environment, Acta Medica Mediterranea, 2016, 32: 587.
G. Craciun, M. Feinberg and Y. Tang, Understanding bistability in complex enzyme-driven reaction networks, Proc. Nat. Acad. Sci. USA 103 (2006), 8697-8702.