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2 In this paper we present the foundation of a unified, object-oriented, three-dimensional (3D) biomodeling environment, which allows us to integrate multiple submodels at scales from subcellular to tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model (CPM), with a continuum reaction-diffusion (RD) model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb. Keywords