Petri Nets, ODEs, and Biochemical Modeling

[TOC]

Fluid Petri-nets

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.