On the development of reactive systems
Logics and models of concurrent systems
Executable object modeling with statecharts
Proceedings of the 18th international conference on Software engineering
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
Cell modeling with reusable agent-based formalisms
Applied Intelligence
Ten top reasons for systems biology to get into model-driven engineering
Proceedings of the 2006 international workshop on Global integrated model management
Discrete Modelling of the Ethylene-Pathway
ICDEW '05 Proceedings of the 21st International Conference on Data Engineering Workshops
Embryonics: A Path to Artificial Life?
Artificial Life
GemCell: A generic platform for modeling multi-cellular biological systems
Theoretical Computer Science
Electronic Notes in Theoretical Computer Science (ENTCS)
Toward Verified Biological Models
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Generic Reactive Animation: Realistic Modeling of Complex Natural Systems
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Robotics and Autonomous Systems
Probabilistic model checking of complex biological pathways
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Abstract machines of systems biology
Transactions on Computational Systems Biology III
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Complex biological systems involve incorporated behaviors of numerous processes, mechanisms and objects. However, experimental analysis, by its nature, divides biological systems into static interactions with little dynamics. To bridge the gap between experimental data and the underlying behavior, our group has been formalizing biological findings into mathematically and algorithmically rigorous specifications, which are then compiled into reactive models. To realistically animate our models, we designed a generic architecture for the earlier idea of reactive animation, in a way that allows it to link up reactive models with animation tools. Here, we describe the reactive animation approach and some of the benefits of employing it to simulate and analyze complex biological systems. We illustrate our approach with a model of pancreatic development, a highly complex system with a unique 3D structure, and also mention more recent work on adding animation to the generic cell project (GemCell).