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 …

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 …

BioNetGen allows a user to create a computational model that characterizes the dynamics of
a signal transduction system, and that accounts comprehensively and precisely for specified …

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 …

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 …

We introduce a graph-theoretic formalism suitable for modeling biochemical networks
marked by combinatorial complexity, such as signal-transduction systems, in which protein …

Modelers of molecular signaling networks must cope with the combinatorial explosion of
protein states generated by posttranslational modifications and complex formation. Rule …

Motivation: In order to aid in hypothesis-driven experimental gene discovery, we are
designing a computer application for the automatic retrieval of signal transduction data from …

Background Rule-based modeling (RBM) is a powerful and increasingly popular approach
to modeling cell signaling networks. However, novel visual tools are needed in order to …

Background Proteins, individual cells, and cell populations denote different levels of an
organizational hierarchy, each of which with its own dynamics. Multi-level modeling is …