Petri nets in VANTED: Simulation of Barley Seed Metabolism

3rd International Workshop on Biological Processes & Petri Nets, a satellite event of PETRI NETS 2012

Anja Hartmann ; Hendrik Rohn ; Kevin Pucknat ; Falk Schreiber

Others  :  http://ceur-ws.org/Vol-852/paper4.pdf
PID  :  43080

来源: CEUR

【 摘 要 】

Petri nets are a mathematical language, which provide a unified environment for modeling, simulation, and formal analysis of biological systems. To support the applicability of Petri nets for biological users we implemented a Petri net add-on for the widely used Vanted framework. Vanted supports Petri net reconstruction, simulation capabilities to be able to investigate dynamic system behavior, and analysis algorithms for calculating intrinsic net properties. Vanted furthermore supports advanced visualization and exploration techniques, which can be used to examine even larger Petri nets in an interactive manner. We use this framework for the simulation-based analysis of a large stoichiometric model of central barley seed metabolism and discuss problems and obstacles during this process.