Part I: Foundations
Introduction
Ina Koch and Falk Schreiber
Biochemical Fundamentals
Tiina Liiving, Syed M. Baker, and Björn H. Junker
Petri Nets
Wolfgang Reisig
Part II: Modeling Techniques
Discrete Modeling
Andrea Sackmann
Modeling Genetic Regulatory Networks
Richard Banks, Victor Khomenko, and L. Jason Steggles
Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling
Ayumu Saito, Masao Nagasaki, Hiroshi Matsuno, and Satoru Miyano
Stochastic Modeling
Ivan Mura
Quantitative Analysis
Jörg Ackermann and Ina Koch
Fuzzy Modeling
Florian Erhard, Lukas Windhager, and Ralf Zimmer
Part III: Biochemical Applications
Topological Analysis of Metabolic and Regulatory Networks
Stefan Schuster and Björn H. Junker
Analysis of Dynamical Models of Signaling Networks with Petri Nets and Dynamic Graphs
Simon Hardy and Ravi Iyengar
A Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets
Claudine Chaouiya, Hanna Klaudel, and Franck Pommereau
A Case Study of HFPN Simulation: Finding Essential Roles of Ror Gene in the Interaction of Feedback Loops in Mammalian Circadian Clock
Hiroshi Matsuno
Prediction of Network Structure
Annegret Wagler
