Statecharts: A visual formalism for complex systems
Science of Computer Programming
Communications of the ACM
On the development of reactive systems
Logics and models of concurrent systems
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
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
Current Trends in Theoretical Computer Science: The Challenge of the New Century
Current Trends in Theoretical Computer Science: The Challenge of the New Century
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In comprehensive modeling the main purpose is to understand an entire biological system in detail, utilizing in the modeling effort all that is known about the system, and to use that understanding to analyze and predict behavior in silico. In realistic modeling the main issue is to model the behavior of actual elements, making possible totally interactive and modifiable realistic executions/simulations that reveal emergent properties. I will address the motivation for such modeling and the philosophy underlying the techniques for carrying it out, as well as the crucial question of when such models are to be deemed valid, or complete. The examples I will present will be from among the biological modeling efforts my group has been involved in: T cell development in the thymus, lymph node behavior, embryonic development of the pancreas, the C. elegans reproduction system and a generic cell model.