Multiple instances and symbolic variables in executable sequence charts
OOPSLA '02 Proceedings of the 17th ACM SIGPLAN conference on Object-oriented programming, systems, languages, and applications
Smart Play-out of Behavioral Requirements
FMCAD '02 Proceedings of the 4th International Conference on Formal Methods in Computer-Aided Design
LSCs: Breathing Life into Message Sequence Charts
Proceedings of the IFIP TC6/WG6.1 Third International Conference on Formal Methods for Open Object-Based Distributed Systems (FMOODS)
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)
Playing with Time: On the Specification and Execution of Time-Enriched LSCs
MASCOTS '02 Proceedings of the 10th IEEE International Symposium on Modeling, Analysis, and Simulation of Computer and Telecommunications Systems
Specifying and executing requirements: the play-in/play-out approach
OOPSLA '02 Companion of the 17th annual ACM SIGPLAN conference on Object-oriented programming, systems, languages, and applications
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
A grand challenge: full reactive modeling of a multi-cellular animal
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
OOPSLA '03 Companion of the 18th annual ACM SIGPLAN conference on Object-oriented programming, systems, languages, and applications
Combining analysis and synthesis in a model of a biological cell
Proceedings of the 2004 ACM symposium on Applied computing
Cell Modeling Using Agent-Based Formalisms
AAMAS '04 Proceedings of the Third International Joint Conference on Autonomous Agents and Multiagent Systems - Volume 3
Smart Play-Out Extended: Time and Forbidden Elements
QSIC '04 Proceedings of the Quality Software, Fourth International Conference
Cell modeling with reusable agent-based formalisms
Applied Intelligence
Comprehensive and realistic modeling of biological systems
Proceedings of the 38th conference on Winter simulation
Symbolic modeling of signal transduction in pathway logic
Proceedings of the 38th conference on Winter simulation
Proceedings of the 38th conference on Winter simulation
Challenges for modeling and simulation methods in systems biology
Proceedings of the 38th conference on Winter simulation
A Probabilistic Model for Molecular Systems
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
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)
Toward Verified Biological Models
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Visualizing inter-dependencies between scenarios
Proceedings of the 4th ACM symposium on Software visualization
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
What Can Formal Methods Bring to Systems Biology?
FM '09 Proceedings of the 2nd World Congress on Formal Methods
FASE'07 Proceedings of the 10th international conference on Fundamental approaches to software engineering
"Don't care" modeling: a logical framework for developing predictive system models
TACAS'07 Proceedings of the 13th international conference on Tools and algorithms for the construction and analysis of systems
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
The calculus of looping sequences
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Abstract interpretation based verification of temporal properties for BioAmbients
Information and Computation
Periodic orbits and equilibria in glass models for gene regulatory networks
IEEE Transactions on Information Theory - Special issue on information theory in molecular biology and neuroscience
Model-checking behavioral programs
EMSOFT '11 Proceedings of the ninth ACM international conference on Embedded software
Software and Systems Modeling (SoSyM)
A new occurrence counting analysis for bioambients
APLAS'05 Proceedings of the Third Asian conference on Programming Languages and Systems
Multiple representations of biological processes
Transactions on Computational Systems Biology VI
SMTT'03 Proceedings of the 2003 international conference on Scenarios: models, Transformations and Tools
Towards reusing model components in systems biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
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
Discrete event multi-level models for systems biology
Transactions on Computational Systems Biology I
An analysis for proving temporal properties of biological systems
APLAS'06 Proceedings of the 4th Asian conference on Programming Languages and Systems
A Probabilistic Model for Molecular Systems
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
Synthesis of biological models from mutation experiments
POPL '13 Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages
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We present preliminary results of a new approach to the formal modeling of biological phenomena. The approach stems from the conceptual compatibility of the methods and logic of data collection and analysis in the field of developmental genetics with the languages, methods and tools of scenario-based reactive system design. In particular, we use the recently developed methodology consisting of the language of live sequence charts with the play-in/play-out process, to model the well-characterized process of cell fate acquisition during C. elegans vulval development.