In silico experimental systems for cell biologists

Jem Rashbass

Advances in computer technology have led to the development of complex simulation environments that can be used by biologists with little computing expertise. These so-called in silico systems allow the experimental scientist in the laboratory to program cellular automata with biological functions in a large number of ways using graphical user interfaces. Automata with a number of different biological properties can then be combined and allowed to 'develop' through a number of biological iterations to produce a simulacrum of a range of cellular phenomena.

Two systems will be described. The first is a morphological modelling environment, the Biological Toolbox, that uses a new computer language Cell Description Language and a web-based interface to define the spatial array of different cells, any secreted morphogens and their gradients, and a number of biological responses. Cell movement and differentiation is calculated on a rule-based system defined by the user and the results computed over time are displayed as a movie. In the second model, Immunosim, quantitative data of cell numbers, diffusable molecules and cell cycle parameters is entered into an in silico system written in JAVA and the environment calculates the growth and differentiation of different cell lineages. The results are then given as a fluorescent activated cell sorter plot that allows direct comparison with wet-lab experiments. The theoretical and practical aspects of these model systems will be discussed.

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