This tool enables biologists and modelers to construct high-level theories and models of biological systems, capturing biological hypotheses, inferred mechanisms, and experimental results within the same framework. Among the key features of the tool are convenient ways to represent several competing theories and the interactive nature of building and running the models using an intuitive, rigorous scenario-based visual language.
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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.
Screenshots and Videos
- Hillel Kugler, Cory Plock, and Andy Roberts, Synthesizing Biological Theories, in Computer Aided Verification (CAV'11), Springer Verlag, July 2011.
- Aleks Milicevic and Hillel Kugler, Model Checking Using SMT and Theory of Lists , in Nasa Formal Methods Symposium , Springer Verlag, April 2011.
- 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.
- H. Kugler, C. Plock, and A. Pnueli, Controller Synthesis from LSC Requirements, in Fundamental Approaches to Software Engineering (FASE'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, vol. 323, no. 1, pp. 1-5, Elsevier , August 2008.
- H. Kugler, A. Larjo, and D. Harel, Biocharts: A Visual Formalism for Complex Biological Systems, in Journal of the Royal Society Interface, vol. 7, no. 48, pp. 1015-1024, July 2010.
- D. Harel, I. Segall, H. Kugler, and Y. Setty, Crafting Game-Models using Reactive System Design , in Future Play, Association for Computing Machinery, Inc., November 2008.
- 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, pp. 157-175, Springer Verlag, March 2008.