GEISHA SYSTEM: An Environment for Simulating Protein Interaction

Abstract Biological analysis of Drosophila embryogenesis has provided a model of protein interaction in segment formation. In this paper we introduce GEISHA system, which verifies and revises the rules of pattern formation in embryogenesis. The system consists of three parts: rule-based simulator, evaluator, and user interface. The simulator tests all the possible rule patterns, and the evaluator qualitatively evaluates results of the simulator; it searches for the desired pattern of protein expression. The user interface enables us to input or save data using GUI. 1 Introduction Many biological systems and their functions came known in the recent prosperity of molecular biology. One of the widely believed concepts is that of a genetic switch, the function of DNA-binding protein, which turns on or off its function; this protein binds to a specific DNA-site, and promotes or represses the transcription of other proteins. The network of DNA-binding proteins is found in many parts of biological systems. The segment formation in the embryo of Drosophila melanogaster (D. melanogaster), a kind of fruitfly, embodies a good example of this interaction of DNA-binding proteins which are translated from segmentation genes. These segmentation proteins specify each segment, which later evolves into a designated part of an imago (adult). So far, biologists found more than 30 proteins relating this segmentation, and now they establish the rough model of interaction among proteins. Many factors relating segmentation, however, are still unknown