Rewriting logic is a simple computational logic that can naturally express both concurrent
computation and logical deduction with great generality. This paper provides a gentle …

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 …

This chapter describes some existing Maude-based tools that are available for download.
The first section describes tools concerned with analysis of either Maude specifications, or of …

Rewriting logic is both a flexible semantic framework within which widely different concurrent
systems can be naturally specified and a logical framework in which widely different logics …

Reductionist science produces causal models of small fragments of complicated systems.
Causal models of entire systems can be hard to construct because what is known of them is …

We present a method for generating a biochemical reaction network from a description of the
interactions of components of biomolecules. The interactions are specified in the form of …

We are witnessing the growing menace of both increasing cases of drug-sensitive and drug-
resistant Mycobacterium tuberculosis strains and the challenge to produce the first new …

Abstract Models that capture the chemical kinetics of cellular regulatory networks can be
specified in terms of rules for biomolecular interactions. A rule defines a generalized …

How do living cells compute and control themselves, and communicate with their
environment? We describe the modeling and analysis of dynamic and reactive biological …

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