A Logic Computational Framework to Query Dynamics on Complex Biological Pathways

摘要

Biological pathways define complex interaction networks where multiple molecular elements work in a series of reactions to produce a response to different biomolecular signals. These biological systems are dynamic and we need mathematical methods that can analyze symbolic elements and complex interactions between them to produce adequate readouts of such systems. Rewriting logic procedures are adequate tools to handle dynamic systems which are applied to the study of specific biological pathways behaviour. Pathway Logic is a rewriting logic development applied to symbolic systems biology. Rewriting logic language Maude allows us to define transition rules and to set up queries about the flow in the biological system. In this paper we describe the use of Pathway Logic to model and analyze the dynamics in a well-known signaling transduction pathway: epidermal growth factor (EGF) pathway. We also use Pathway Logic Assistant (PLA) tool to browse and query this system.