We have developed methods and systems for analyzing epigenetic information in cells, as well as that of genetic information, to expand our understanding of how living systems are determined. Because cells are minimum units reflecting epigenetic information, which is considered to map the history of a parallel-processing recurrent network of biochemical reactions, their behaviors cannot be explained by considering only conventional DNA informationprocessing events. The role of epigenetic information in cells, which complements their genetic information, was inferred by comparing predictions from genetic information with cell behavior observed under conditions chosen to reveal adaptation processes and community effects. A system for analyzing epigenetic information was developed starting from the twin complementary viewpoints of cell regulation as an 'algebraic' system (emphasis on temporal aspects) and as a 'geometric' system (emphasis on spatial aspects). The knowledge acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.