Scenario-Based Tool for Biological Modeling
Studies of biological systems are often facilitated by diagram “models” that summarize the current understanding of underlying mechanisms. The increasing complexity of our understanding of Biology necessitates computational models that can extend these representations to include their dynamic behavior. The Scenario-Based Tool aims to provide a scalable and intuitive tool for biological modeling, where the main modeling construct is a “scenario”, a story about the system. A main objective is to make the tool intuitive for Biologists and user friendly, and on the other hand develop and integrate powerful simulation, analysis and visualization methods to support effective ways to probe the biological models and enable predicitive capabilities.
- H. Kugler and I. Segall, Compositional Synthesis of Reactive Systems from Live Sequence Chart Specifications, in Tools and Algorithms for the Construction and Analysis of Systems (TACAS'09), Springer Verlag, March 2009
- Kam N., Kugler H., Marelly R., Appleby L., Fisher J., A. Pnueli, D. Harel, M.J. Stern, and E.J.A. Hubbard, A scenario-based approach to modeling development: A prototype model of C. elegans vulval fate specification , in Developmental Biology, Elsevier , August 2008
- Harel, D., Segall, I., Kugler, H., Setty, and Y., Crafting Game-Models using Reactive System Design , in Future Play, Association for Computing Machinery, Inc., November 2008
- H. Kugler, C. Plock, and A. Pnueli, Controller Synthesis from LSC Requirements, in Fundamental Approaches to Software Engineering (FASE'09), Springer Verlag, March 2009
- D. Harel, H. Kugler, S. Maoz, and I. Segall, How Hard is Smart Play-Out? On the Complexity of Verification-Driven Execution, in Perspectives in Concurrency Theory (Festschrift for P.S. Thiagarajan), (K. Lodaya et al, eds.), University Press (India), 2009
- P. Combes, D. Harel, and H. Kugler, Modeling and Verification of a Telecommunication Application using Live Sequence Charts and the Play-Engine Tool, in Software and Systems Modeling, vol. 7, no. 2, March 2008
