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 …

Membrane computing is a vibrant and fast-growing research area of natural computation
which covers the study of computing models, called membrane systems or P systems …

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 …

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 …

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

We introduce a family of process calculi with dynamic nested membranes. In contrast to
related calculi, including some developed for biological applications, active entities here are …

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

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 …