Statecharts: A visual formalism for complex systems
Science of Computer Programming
Conditional rewriting logic as a unified model of concurrency
Selected papers of the Second Workshop on Concurrency and compositionality
A petri net application to model metabolic processes
Systems Analysis Modelling Simulation
LSCs: Breathing Life into Message Sequence Charts
Formal Methods in System Design
Information Processing Letters
Communication and Concurrency
Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
The Immune System as a Reactive System: Modeling T Cell Activation With Statecharts
HCC '01 Proceedings of the IEEE 2001 Symposia on Human Centric Computing Languages and Environments (HCC'01)
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
PRISM: a tool for automatic verification of probabilistic systems
TACAS'06 Proceedings of the 12th international conference on Tools and Algorithms for the Construction and Analysis of Systems
Analyzing pathways using SAT-based approaches
AB'07 Proceedings of the 2nd international conference on Algebraic biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
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Pathway Logic is a step towards a vision of symbolic systems biology. It is an approach to modeling cellular processes based on formal methods. In particular, formal executable models of processes such as signal transduction, metabolic pathways, and immune system cell-cell signaling are developed using the rewriting logic language Maude and a variety of formal tools are used to query these models. An important objective of Pathway Logic is to reflect the ways that biologists think about problems using informal models, and to provide bench biologists with tools for computing with and analyzing these models that are natural. In this paper we describe the Pathway Logic approach to the modeling and analysis of signal transduction, and the use of the Pathway Logic Assistant tool to browse and query these models. The Rac1 signaling pathway is used to illustrate the concepts.