Physicochemical modelling of signal transduction links fundamental chemical and physical
principles, prior knowledge about regulatory pathways, and experimental data of various …

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 …

BioNetGen is an open-source software package for rule-based modeling of complex
biochemical systems. Version 2.2 of the software introduces numerous new features for both …

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 …

Mathematical equations are fundamental to modeling biological networks, but as networks
get large and revisions frequent, it becomes difficult to manage equations directly or to …

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

Abstract Systems Biology has taken advantage of computational tools and high-throughput
experimental data to model several biological processes. These include signaling, gene …

The Mitogen-Activated Protein Kinase (MAPK) network consists of tightly interconnected
signalling pathways involved in diverse cellular processes, such as cell cycle, survival …

The Virtual Cell (VCell; http://vcell. org/) is a problem solving environment, built on a central
database, for analysis, modelling and simulation of cell biological processes. VCell …

Crosstalk mechanisms have not been studied as thoroughly as individual signaling
pathways. We exploit experimental and computational approaches to reveal how a …