The interdisciplinary study of coordination
ACM Computing Surveys (CSUR)
Model checking
Reo: a channel-based coordination model for component composition
Mathematical Structures in Computer Science
Formal Methods for Components and Objects: First International Symposium, Fmco 2002, Leiden, the Netherlands, November 2002: Revised Lectures (Lecture Notes in Computer Science, 2852)
Models and Temporal Logics for Timed Component Connectors
SEFM '04 Proceedings of the Software Engineering and Formal Methods, Second International Conference
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
PML: Toward a High-Level Formal Language for Biological Systems
Electronic Notes in Theoretical Computer Science (ENTCS)
Formal Molecular Biology Done in CCS-R
Electronic Notes in Theoretical Computer Science (ENTCS)
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Symbolic Model Checking for Channel-based Component Connectors
Electronic Notes in Theoretical Computer Science (ENTCS)
A Basic Logic for Reasoning about Connector Reconfiguration
Fundamenta Informaticae - Behavior of Composed Concurrent Systems: Logic and Reasoning
Design Issues for Qualitative Modelling of Biological Cells with Petri Nets
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Symbolic model checking for channel-based component connectors
Science of Computer Programming
Biomolecular Agents as Multi-behavioural Concurrent Objects
Electronic Notes in Theoretical Computer Science (ENTCS)
Comparing three coordination models: Reo, ARC, and PBRD
Science of Computer Programming
Formal modeling
Synthesis of reo circuits for implementation of component-connector automata specifications
COORDINATION'05 Proceedings of the 7th international conference on Coordination Models and Languages
Stochastic reasoning about channel-based component connectors
COORDINATION'06 Proceedings of the 8th international conference on Coordination Models and Languages
Symbolic execution of Reo circuits using constraint automata
Science of Computer Programming
A Basic Logic for Reasoning about Connector Reconfiguration
Fundamenta Informaticae - Behavior of Composed Concurrent Systems: Logic and Reasoning
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We present an application of the Reo coordination paradigm to provide a compositional formal model for describing and reasoning about the behaviour of biological systems, such as regulatory gene networks. Reo governs the interaction and flow of data between components by allowing the construction of connector circuits which have a precise formal semantics. When applied to systems biology, the result is a graphical model, which is comprehensible, mathematically precise, and flexible.