This invention describes a computer-based system (112), methods and visual interfaces for providing an integrated development and deployment framework for visual modeling and dynamic simulation of virtual models of complex systems, which can be further integrated with monitoring (108) and control (138) devices to monitor and control the operation of the complex systems modeled (102) and can be used for information retrieval. More particularly, the virtual models in the present invention relate to visual models of biochemical complex systems, comprising sets of icons representing processes and their participants linked into multidimensional pathways (116), further organized in a hierarchy of icons representing discrete time and space compartments, wherein such compartments may contain other compartments, and wherein those modular icons encapsulate in different layers all the information, data, and mathematical models that characterize and define each virtual model.
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