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
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
LSCs: Breathing Life into Message Sequence Charts
Formal Methods in System Design
Information Processing Letters
Communication and Concurrency
Membrane Computing: An Introduction
Membrane Computing: An Introduction
Introduction to General Net Theory
Proceedings of the Advanced Course on General Net Theory of Processes and Systems: Net Theory and Applications
Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
LICS '96 Proceedings of the 11th Annual IEEE Symposium on Logic in Computer Science
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
Symbolic modeling of signal transduction in pathway logic
Proceedings of the 38th conference on Winter simulation
Control Flow Analysis for BioAmbients
Electronic Notes in Theoretical Computer Science (ENTCS)
Abstractions for hybrid systems
Formal Methods in System Design
Formal Executable Models of Cell Signaling Primitives
ISOLA '06 Proceedings of the Second International Symposium on Leveraging Applications of Formal Methods, Verification and Validation
ICATPN'00 Proceedings of the 21st international conference on Application and theory of petri nets
Automated symbolic reachability analysis: with application to delta-notch signaling automata
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
Analyzing pathways using SAT-based approaches
AB'07 Proceedings of the 2nd international conference on Algebraic biology
A unifying framework for modelling and analysing biochemical pathways using Petri nets
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
All about maude - a high-performance logical framework: how to specify, program and verify systems in rewriting logic
Abstract machines of systems biology
Transactions on Computational Systems Biology III
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Quantitative Pathway Logic for Computational Biology
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
The κ-Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
A Graphical User Interface for Maude-NPA
Electronic Notes in Theoretical Computer Science (ENTCS)
Understanding signalling networks as collections of signal transduction pathways
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Compositional modelling of signalling pathways in timed concurrent constraint programming
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Programming in Biomolecular Computation
Electronic Notes in Theoretical Computer Science (ENTCS)
TLCA'11 Proceedings of the 10th international conference on Typed lambda calculi and applications
Backward trace slicing for rewriting logic theories
CADE'11 Proceedings of the 23rd international conference on Automated deduction
Honoring Carolyn Talcott's contributions to science
Formal modeling
Computational biology: a programming perspective
Formal modeling
Using conditional trace slicing for improving Maude programs
Science of Computer Programming
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Pathway Logic (PL) is an approach to modeling and analysis of biological processes based on rewriting logic. This tutorial describes the use of PL to model signal transduction processes. It begins with a general discussion of Symbolic Systems Biology, followed by some background on rewriting logic and signal transduction. The representation and analysis of a small model Ras and Raf activation is presented in some detail. This is followed by discussion of a curated model of early signaling events in response to Epidermal Growth Factor stimulation.