Abstract: A computer based virtual models of complex systems, together with integrated systems and methods provide a development and execution framework for visual modeling and dynamic simulation of said models. The virtual models can be used for analysis, monitoring, or control of the operation of the complex systems modeled, as well as for information retrieval. More particularly, the virtual models in the present implementation relate to biological complex systems. In the current implementation the virtual models comprise building blocks representing physical, chemical, or biological processes, the pools of entities that participate in those processes, a hierarchy of compartments representing time-intervals or the spatial and/or functional structure of the complex system in which said entities are located and said processes take place, and the description of the composition of those entities.

Abstract: This invention describes computer based systems and methods for modeling and simulation of biochemical networks of pathways, including metabolic, signal transduction and regulatory pathways within a cell or across cells. The invention comprises systems and methods for building the models and for using the models for analysis and information retrieval, for determining the effect that modulating one or more reactions in a biochemical pathway has on an operation of the biochemical pathway, and for simulating or predicting an altered physiological state of cells.

Abstract: This invention describes computer based systems and methods for modeling and simulation of complex biological systems from the cellular, or subcellular, to the organism and population level, for using said models to predict functions of components of the biological systems and to simulate physiological and pathological states at the various levels, and for using said models in drug development for testing in a computer system substances for possible use as therapeutics by simulating their effects on the physiological and pathological states.

Abstract: This invention describes computer based virtual models of complex systems, together with integrated systems and methods providing a development and execution framework for visual modeling and dynamic simulation of said models. The virtual models can be used for analysis, monitoring, or control of the operation of the complex systems modeled, as well as for information retrieval. More particularly, the virtual models in the present implementation relate to biological complex systems. In the current implementation the virtual models comprise building blocks representing physical, chemical, or biological processes, the pools of entities that participate in those processes, a hierarchy of compartments representing time-intervals or the spatial and/or functional structure of the complex system in which said entities are located and said processes take place, and the description of the composition of those entities.

Abstract: The present invention describes an integrated computer-based graphical interface, methods and systems providing a shell environment for development and deployment for graphic information storage and retrieval, visual modeling and dynamic simulation of complex systems. In the current implementation the system comprises libraries of knowledge-based building-blocks that include sets of icons representing chemical processes, the pools of entities that participate in those processes, and the graphical description of those entities, encapsulating both information and mathematical models within the modular components, in the form of tables and in the form of component icons, and a plurality of methods are associated with each of the icons. The models are built by interconnecting each pool to one or several processes, and each process to one or several pools, resulting in complex networks of multidimensional pathways.

Abstract: The present invention describes an integrated computer-based system, methods, and graphical interfaces, providing an environment for development and deployment of visual models of complex systems organized in discrete time and space compartments, used for graphic information storage and retrieval, visual modeling and dynamic simulation of said complex systems. In the current implementation the system comprises libraries of knowledge-based building-blocks that include sets of icons representing chemical processes, the pools of entities that participate in those processes, and the graphical description of those entities, encapsulating both information and mathematical models within the modular components, in the form of attributes or in the form of component icons, and a plurality of methods are associated with each of the icons. The models are built by linking each pool to one or several processes, and each process to one or several pools, resulting in complex networks of multidimensional pathways.