Formalized rules for protein-protein interactions have recently been introduced to represent
the binding and enzymatic activities of proteins in cellular signaling. Rules encode an …

In this paper, kinetic modeling techniques for complex chemical processes are reviewed.
After a brief historical overview of chemical kinetics, an overview is given of the theoretical …

Rule-based modeling involves the representation of molecules as structured objects and
molecular interactions as rules for transforming the attributes of these objects. The approach …

Modelling is becoming a necessity in studying biological signalling pathways, because the
combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms …

Rule‐based modeling was developed to address the limitations of traditional approaches for
modeling chemical kinetics in cell signaling systems. These systems consist of multiple …

Given the combinatorial nature of cellular signalling pathways, where biological agents can
bind and modify each other in a large number of ways, concurrent or agent-based …

The input and output formats, and the structure of Rule Input Network Generator (RING), a
computational tool for generation and analysis of complex reaction networks, are described …

We introduce a reversible process calculus with a new feature of execution control that
allows us to change the direction and pattern of computation. This feature allows us to model …

We present a kinetic Monte Carlo method for simulating chemical transformations specified
by reaction rules, which can be viewed as generators of chemical reactions, or equivalently …

We present an algorithm, called BioLab, for verifying temporal properties of rule-based
models of cellular signalling networks. BioLab models are encoded in the BioNetGen …