Petri Nets, ODEs, and Biochemical Modeling

Fluid Petri-nets

• Horton, Graham, Vidyadhar G. Kulkarni, David M. Nicol, and Kishor S. Trivedi. "Fluid Stochastic Petri Nets: Theory, Applications, and Solution." (1996).
• Silva, Manuel, and Laura Recalde. "On fluidification of Petri Nets: from discrete to hybrid and continuous models." Annual Reviews in Control 28, no. 2 (2004): 253-266.
• Ciardo, Gianfranco, David M. Nicol, and Kishor Shridharbhai Trivedi. "Discrete-event simulation of fluid stochastic Petri nets." IEEE transactions on software engineering 25, no. 2 (1999): 207-217.
• Tuffin, Bruno, Dong S. Chen, and Kishor S. Trivedi. "Comparison of hybrid systems and fluid stochastic Petri nets." Discrete Event Dynamic Systems 11, no. 1-2 (2001): 77-95.
• Horton, Graham, Vidyadhar G. Kulkarni, David M. Nicol, and Kishor S. Trivedi. "Fluid stochastic Petri nets: Theory, applications, and solution techniques." European Journal of Operational Research 105, no. 1 (1998): 184-201.

Petri-nets for Biochemical Modeling

• Heiner, Monika, David Gilbert, and Robin Donaldson. "Petri nets for systems and synthetic biology." In International school on formal methods for the design of computer, communication and software systems, pp. 215-264. Springer, Berlin, Heidelberg, 2008.
• Gilbert, David, and Monika Heiner. "From Petri nets to differential equations–an integrative approach for biochemical network analysis." In International Conference on Application and Theory of Petri Nets, pp. 181-200. Springer, Berlin, Heidelberg, 2006.
• Galpin, Vashti. "Continuous approximation of PEPA models and Petri nets." International Journal of Computer Aided Engineering and Technology 2, no. 4 (2010): 324-339.
  • Slides
• Hardy, Simon, and Pierre N. Robillard. "Modeling and simulation of molecular biology systems using petri nets: modeling goals of various approaches." Journal of bioinformatics and computational biology 2, no. 04 (2004): 619-637.
• Gilbert, David, Monika Heiner, and Sebastian Lehrack. "A unifying framework for modelling and analysing biochemical pathways using Petri nets." In International Conference on Computational Methods in Systems Biology, pp. 200-216. Springer, Berlin, Heidelberg, 2007.