Statecharts: A visual formalism for complex systems
Science of Computer Programming
Model checking
LSCs: Breathing Life into Message Sequence Charts
Formal Methods in System Design
Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Scenario-Based Monitoring and Testing of Real-Time UML Models
«UML» '01 Proceedings of the 4th International Conference on The Unified Modeling Language, Modeling Languages, Concepts, and Tools
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)
Come, Let's Play: Scenario-Based Programming Using LSC's and the Play-Engine
Come, Let's Play: Scenario-Based Programming Using LSC's and the Play-Engine
InterPlay: Horizontal Scale-Up and Transition to Design in Scenario-Based Programming
IEEE Transactions on Software Engineering
Proceedings of the 38th conference on Winter simulation
A&A for modelling and engineering simulations in Systems Biology
International Journal of Agent-Oriented Software Engineering
Toward Verified Biological Models
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An extendable system for conceptual modeling and simulation of signal transduction pathways
ER'07 Proceedings of the 2007 conference on Advances in conceptual modeling: foundations and applications
Some results on the expressive power and complexity of LSCs
Pillars of computer science
Programming coordinated behavior in java
ECOOP'10 Proceedings of the 24th European conference on Object-oriented programming
Behavioral programming, decentralized control, and multiple time scales
Proceedings of the compilation of the co-located workshops on DSM'11, TMC'11, AGERE!'11, AOOPES'11, NEAT'11, & VMIL'11
Synthesis revisited: generating statechart models from scenario-based requirements
Formal Methods in Software and Systems Modeling
Transactions on Computational Systems Biology VII
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Biological systems have recently been shown to share many of the properties of reactive systems. This observation has led to the idea of using methods devised for the construction (engineering) of complex reactive systems to the modeling (reverse-engineering) of biological systems, in order to enhance biological comprehension. Here we suggest to combine the two formal approaches used in our group — the state-based formalism of statecharts and the scenario-based formalism of live sequence charts (LSCs). We propose that biological observations are better formalized in the form of LSCs, while biological mechanistic models would be more natural to specify using statecharts. Combining the two approaches would enable one to verify the proposed mechanistic models against the real data. The biological observations can be compared to the requirements in an engineered system, and the mechanistic model would be analogous to the implementation. While requirements are used to design an implementation, here the observations are used to motivate the invention of the mechanistic model. In both cases consistency of one with the other must be established, by testing or by formal verification.