Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Symbolic modeling of signal transduction in pathway logic
Proceedings of the 38th conference on Winter simulation
Proceedings of the 38th conference on Winter simulation
Theoretical Computer Science
Statecharts in the making: a personal account
Proceedings of the third ACM SIGPLAN conference on History of programming languages
Formal Molecular Biology Done in CCS-R
Electronic Notes in Theoretical Computer Science (ENTCS)
GemCell: A generic platform for modeling multi-cellular biological systems
Theoretical Computer Science
Toward Verified Biological Models
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Analysing formal models of genetic regulatory networks with delays
International Journal of Bioinformatics Research and Applications
Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Modeling biological reactivity: statecharts vs. Boolean logic
Proceedings of the Working Conference on Advanced Visual Interfaces
PLAZZMID: an evolutionary agent-based architecture inspired by Bacteria and Bees
ECAL'07 Proceedings of the 9th European conference on Advances in artificial life
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
Authoring and verification of clinical guidelines: A model driven approach
Journal of Biomedical Informatics
Some thoughts on the semantics of biocharts
Time for verification
Multiple representations of biological processes
Transactions on Computational Systems Biology VI
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
Virtualization in systems biology: metamodels and modeling languages for semantic data integration
Transactions on Computational Systems Biology I
Translating SBML models into the stochastic π-calculus for stochastic simulation
Transactions on Computational Systems Biology VII
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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The construction of reliable reactive systems isconsidered to be one of the most challenging goals in thefields of software and system engineering.The definitionof a reactive system suits biological systems at differentlevels, ranging from gene networks, developing embryosand the immune system.We report here the application ofa tool developed for constructing computerized systems tothe modeling and analysis of a biological system, theimmune system.We use the language of statecharts withinthe framework of object-oriented modeling.The resultsdescribed here indicate that this modeling strategy cancontribute to the transition of biology from the phase ofanalysis to the phase of synthesis.