17 A theory for complex systems: reactive animation

Publisher Summary There is a visually dynamic way to represent and study complex biologic data—reactive animation (RA). Complex system theory amounts to organizing data and representing it in a way that engages the mind to see the data anew and undertake new experiments. A theory for a complex system must simplify and compress data to the point where the system is rendered comprehensible, but the simplification and compression must not go beyond the point at which the essence of the complexity is lost. Humans draw pictures and respond to pictures that resemble the prototypic objects they like to see or have learned to see. The cinema, TV, DVD, the computer screen, and the world of advertising all demonstrate that moving pictures move minds and generate returns. Therefore, RA is built to connect the simulations of Statecharts to traditional representations of cells and molecules in an animated format. RA is created by connecting the Statecharts language and its support tool Rhapsody to the flash system, which is a commonly used software package for programming animation. RA departs from the approaches to biological system modeling developed till now; traditionally, modeling has focused on neat concepts rather than messy data or has abandoned the data entirely to construct artificial and synthetic computations aimed at reproducing in silico ersatz genomes, life-like patterns, or evolving biomorphs.

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