Generic Reactive Animation: Realistic Modeling of Complex Natural Systems

Harel, David; Setty, Yaki

doi:10.1007/978-3-540-68413-8_1

Cited by 10 publications

(11 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Using generic reactive animation (Efroni et al, 2005;Harel and Setty, 2008) we linked the Rhapsody model with a real-time Flash-based front-end (Flash Professional CS3, Adobe). Each object in the simulation is represented as an animated figure, which changes properties such as size and color to designate changes during the lifetime of the object.…”

Section: The Modeling Tools: Statecharts Rhapsody and Reactive Animamentioning

confidence: 99%

A model of stem cell population dynamics: in silico analysis and in vivo validation

et al. 2012

Self Cite

View full text Add to dashboard Cite

SUMMARYThe proper renewal and maintenance of tissues by stem cell populations is simultaneously influenced by anatomical constraints, cell proliferation dynamics and cell fate specification. However, their relative influence is difficult to examine in vivo. To address this difficulty we built, as a test case, a cell-centered state-based computational model of key behaviors that govern germline development in C. elegans, and used it to drive simulations of cell population dynamics under a variety of perturbations. Our analysis provided unexpected possible explanations for laboratory observations, including certain 'all-or-none' phenotypes and complex differentiation patterns. The simulations also offered insights into niche-association dynamics and the interplay between cell cycle and cell fate. Subsequent experiments validated several predictions generated by the simulations. Notably, we found that early cell cycle defects influence later maintenance of the progenitor cell population. This general modeling approach is potentially applicable to other stem cell systems.

show abstract

Section: The Modeling Tools: Statecharts Rhapsody and Reactive Animamentioning

confidence: 99%

A model of stem cell population dynamics: in silico analysis and in vivo validation

et al. 2012

Self Cite

View full text Add to dashboard Cite

show abstract

“…Furthermore, this setup can be easily strengthened by adding more tools. For example, data analysis software (e.g., Matlab or Mathematica) can be integrated to provide real-time analysis of the simulation (e.g., statistics, graphs; as was done in [22]). This setup helps to disclose various potential scenarios and emergence in the model.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, the specifications were linked up with a game engine for run-time analysis. The tools were integrated using a generic platform for reactive animation [12,22], which smoothly links up the reactive models with the animated front-end.…”

Section: The Modeling Approachmentioning

confidence: 99%

Crafting game-models using reactive system design

Harel

Segall

Kugler

et al. 2008

Proceedings of the 2008 Conference on Future Play: Research, Play, Share

Self Cite

View full text Add to dashboard Cite

This paper presents a game-model of a gym training system, where the behavior of the system is specified using languages developed originally for reactive system design, which drive a game engine. The approach makes it possible to describe behaviors of different parts of the system using different reactive system design languages and tools. It thus provides a framework for integrating the model behavior to obtain an executable game-model of the entire system. Among the advantages of this approach is the ability to use existing analysis tools to understand the game behavior at design time and run time, the ability to easily modify the behavior, and the use of visual languages to allow various stakeholders to be involved in early stages of building the game. Finally, we suggest integrating future games and game design methods into the emerging field of biological modeling, to which reactive system design has recently been successfully applied.

show abstract

“…Using a generic platform for Reactive Animation [18], we linked the model to a 3D animated front-end (in 3DGS [1]) and a mathematical GUI (in MATLAB). The front-end visualizes the simulation and provides the means to interact with it, while the mathematical GUI monitors and analyzes the progress.…”

Section: Modeling Approachmentioning

confidence: 99%

“…We linked the model to a 3D animated front-end (in 3DGameStudio [1]) and an analysis GUI (in MATLAB [23]), using the idea of Reactive Animation [10] and its generic platform [18]. At run-time, the simulation is visualized and analyzed at a front-end and a GUI, respectively.…”

Section: Introductionmentioning

confidence: 99%

On Using Divide and Conquer in Modeling Natural Systems

Setty

Cohen

Mayo

et al. 2009

Algorithmic Bioprocesses

Self Cite

View full text Add to dashboard Cite

In recent years, we have been studying approaches to the realistic modeling of natural systems, especially biological systems. We have tested several of these in a project devoted to modeling pancreatic organogenesis, a complex system that dynamically promotes structural and molecular development. Here, we describe one of these approaches-a kind of 'divide and conquer' technique, in which the system is disassembled into modules to specify behaviors on the scale of the organ (i.e., morphogenesis) and the cell (i.e., molecular interactions). At run-time, these modules are re-assembled to direct development in individual cells. This approach employs multi-scaling and dynamics, two important characteristics of natural systems, but avoids cross-scaling. It thus appears to be useful for systems in which the importance of cross-scaling seems to be less significant, such as the development of phyllotaxis in plants. In pancreatic organogenesis, cross-scaling was found to be a significant characteristic, and thus by using 'divide and conquer' we could cover only its preliminary stages. We discuss the approach and our use of it, as well as he various methods to analyze the achievements and limitations of the end result.

show abstract

Generic Reactive Animation: Realistic Modeling of Complex Natural Systems

Cited by 10 publications

References 36 publications

A model of stem cell population dynamics: in silico analysis and in vivo validation

A model of stem cell population dynamics: in silico analysis and in vivo validation

Crafting game-models using reactive system design

On Using Divide and Conquer in Modeling Natural Systems

Contact Info

Product

Resources

About