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Synthesizing Biological Theories

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

Stem Cell population Dynamics


User Guide



Hillel Kugler

Cory Plock

Andy Roberts


Chris McEwan

Aleks Milivevic

Antti Larjo

Itai Segall

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