Statecharts: A visual formalism for complex systems
Science of Computer Programming
On the development of reactive systems
Logics and models of concurrent systems
The temporal logic of reactive and concurrent systems
The temporal logic of reactive and concurrent systems
Model checking
LSCs: Breathing Life into Message Sequence Charts
Formal Methods in System Design
Distributed Algorithms
Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
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
Formalization of the Protein Production by Means of Petri Nets
ICIIS '99 Proceedings of the 1999 International Conference on Information Intelligence and Systems
InterPlay: Horizontal Scale-Up and Transition to Design in Scenario-Based Programming
IEEE Transactions on Software Engineering
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
Combining state-based and scenario-based approaches in modeling biological systems
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
GemCell: A generic platform for modeling multi-cellular biological systems
Theoretical Computer Science
Concurrency in Biological Modeling: Behavior, Execution and Visualization
Electronic Notes in Theoretical Computer Science (ENTCS)
Generic Reactive Animation: Realistic Modeling of Complex Natural Systems
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
A Bayesian Approach to Model Checking Biological Systems
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Qualitative system identification from imperfect data
Journal of Artificial Intelligence Research
What Can Formal Methods Bring to Systems Biology?
FM '09 Proceedings of the 2nd World Congress on Formal Methods
Programming coordinated behavior in java
ECOOP'10 Proceedings of the 24th European conference on Object-oriented programming
Modeling Biology using Generic Reactive Animation
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
Communications of the ACM
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
Communications of the ACM
Maximally Parallel Probabilistic Semantics for Multiset Rewriting
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P)
Probabilistic model checking of the PDGF signaling pathway
Transactions on Computational Systems Biology XIV
TTP: tool for tumor progression
CAV'13 Proceedings of the 25th international conference on Computer Aided Verification
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The last several decades have witnessed a vast accumulation of biological data and data analysis. Many of these data sets represent only a small fraction of the system's behavior, making the visualization of full system behavior difficult. A more complete understanding of a biological system is gained when different types of data (and/or conclusions drawn from the data) are integrated into a larger-scale representation or model of the system. Ideally, this type of model is consistent with all available data about the system, and it is then used to generate additional hypotheses to be tested. Computer-based methods intended to formulate models that integrate various events and to test the consistency of these models with respect to the laboratory-based observations on which they are based are potentially very useful. In addition, in contrast to informal models, the consistency of such formal computer-based models with laboratory data can be tested rigorously by methods of formal verification. We combined two formal modeling approaches in computer science that were originally developed for non-biological system design. One is the inter-object approach using the language of live sequence charts (LSCs) with the Play-Engine tool, and the other is the intra-object approach using the language of statecharts and Rhapsody as the tool. Integration is carried out using InterPlay, a simulation engine coordinator. Using these tools, we constructed a combined model comprising three modules. One module represents the early lineage of the somatic gonad of C. elegans in LSCs, while a second more detailed module in statecharts represents an interaction between two cells within this lineage that determine their developmental outcome. Using the advantages of the tools, we created a third module representing a set of key experimental data using LSCs. We tested the combined statechart-LSC model by showing that the simulations were consistent with the set of experimental LSCs. This small-scale modular example demonstrates the potential for using similar approaches for verification by exhaustive testing of models by LSCs. It also shows the advantages of these approaches for modeling biology.