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 …

Life science researchers use computational models to articulate and test hypotheses about
the behavior of biological systems. Semantic annotation is a critical component for …

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 …

Managing the overwhelming numbers of molecular states and interactions is a fundamental
obstacle to building predictive models of biological systems. Here we introduce the Network …

Word models (natural language descriptions of molecular mechanisms) are a common
currency in spoken and written communication in biomedicine but are of limited use in …

In this work we present Bio-PEPA, a process algebra for the modelling and the analysis of
biochemical networks. It is a modification of PEPA, originally defined for the performance …

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

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 …

Motivation We present an overview of the Kappa platform, an integrated suite of analysis
and visualization techniques for building and interactively exploring rule-based models. The …