The simulation of chemical reacting systems is one of the most challenging topics in Systems Biology, due to their complexity and inherent randomness. The Gillespie's Stochas...
Biochemical pathways, such as metabolic, regulatory, and signal transduction pathways, constitute complex networks of functional and physical interactions between molecular species...
We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms. Each per...
Background: Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem. Result...
We consider a class of systems with a cyclic interconnection structure that arises, among other examples, in dynamic models for certain biochemical reactions. We first show that a...