Abstract: The invention encompasses systems, methods, and apparatus for predicting clinical outcomes and monitoring an individual's response to a therapeutic regimen. The invention further encompasses methods for predicting cardiovascular risk based a genetic marker status and methods for modifying a computer to reflect genetic data and for incorporating genetic markers into a virtual population.

Abstract: An apparatus and method for validating a computer model is described. In one embodiment, a computer-readable medium comprises instructions to associate a set of configurations of a computer model with a stimulus-response test, each configuration of the set of configurations representing a different model scenario, the stimulus-response test defining a modification to each configuration of the set of configurations. The computer-readable medium also comprises instructions to apply the stimulus-response test to the set of configurations to produce a simulated response for each configuration of the set of configurations and instructions to compare the simulated responses for the set of configurations with an expected response to the stimulus-response test.

Abstract: The present invention relates to a mathematical and computer model of a joint. The model includes representation of the biological processes related to the synovial tissue and cartilage. In one embodiment, the model represents a human joint afflicted with rheumatoid arthritis.

Abstract: The invention encompasses novel computer models of atherosclerosis and systems for predicting development and progression of atherosclerosis as well as associated cardiovascular risk. In particular, the computer model of atherosclerosis comprises a) a cholesterol metabolism module; b) an atherogenesis module; and c) a plaque stability module. The computer model optionally further comprises a cardiovascular risk module.

Abstract: The present invention relates generally to a computer model of an adaptive immune response. One embodiment of the invention relates to a computer model of an adaptive immune response within the framework of signals conveyed at the site of antigen exposure. Another embodiment of the model includes a representation of complex physiological regulatory mechanisms related to, for example, cellular dynamics, mediator production, antigen-presenting cell (APC) recruitment, APC maturation, lymphocyte activation, lymphocyte trafficking, and/or lymphocyte effector function. In another embodiment, the model can account for mediator production in response to antigen within a chronically inflamed peripheral tissue, as well as the regulatory effects of mediators on APC and lymphocyte population dynamics, including maturation, activation, and apoptosis, and the regulatory effects of mediators produced by APCs and lymphocytes on a chronically inflamed peripheral tissue.

Abstract: A method of conducting a sequence of linked simulation operations, utilizing a computer-based simulation model, commences with the performance of a first simulation operation to generate an output condition. A further simulation operation, which is defined to sequentially follow the first simulation operation, is then formed utilizing the simulation model. The second simulation operation at least partially and automatically inherits the output condition generated by the first simulation operation as an input condition. In this way, the second simulation operation commences with a configuration captured from a preceding simulation operation as an input condition. Multiple simulation operations may at least partially inherit a configuration from the first simulation operation.

Abstract: A method of conducting a sequence of linked simulation operations, utilizing a computer-based simulation model, commences with the performance of a first simulation operation to generate an output condition. A further simulation operation, which is defined to sequentially follow the first simulation operation, is then formed utilizing the simulation model. The second simulation operation at least partially and automatically inherits the output condition generated by the first simulation operation as an input condition. In this way, the second simulation operation commences with a configuration captured from a preceding simulation operation as an input condition. Multiple simulation operations may at least partially inherit a configuration from the first simulation operation.

Abstract: The present invention relates to a mathematical and computer model of a joint. The model includes representation of the biological processes related to the synovial tissue and cartilage. In one embodiment, the model represents a human joint afflicted with rheumatoid arthritis.

Abstract: An apparatus and method for identifying biomarkers using a computer model is described. In one embodiment, a computer-executable software code includes code to define a set of configurations associated with a computer model of a biological system. The computer-executable software code also includes code to apply a virtual measurement to the set of configurations to produce a result of the virtual measurement for each configuration of the set of configurations and code to apply a virtual therapy to the set of configurations to produce a result of the virtual therapy for each configuration of the set of configurations. The computer-executable software code further includes code to identify correlation between the results of the virtual measurement for the set of configurations and the results of the virtual therapy for the set of configurations.

Abstract: The present invention relates generally to a computer model of an adaptive immune response. One embodiment of the invention relates to a computer model of an adaptive immune response within the framework of signals conveyed at the site of antigen exposure. Another embodiment of the model includes a representation of complex physiological regulatory mechanisms related to, for example, cellular dynamics, mediator production, antigen-presenting cell (APC) recruitment, APC maturation, lymphocyte activation, lymphocyte trafficking, and/or lymphocyte effector function. In another embodiment, the model can account for mediator production in response to antigen within a chronically inflamed peripheral tissue, as well as the regulatory effects of mediators on APC and lymphocyte population dynamics, including maturation, activation, and apoptosis, and the regulatory effects of mediators produced by APCs and lymphocytes on a chronically inflamed peripheral tissue.

Abstract: The present invention relates to a mathematical and computer model of a joint. The model includes representation of the biological processes related to the synovial tissue and cartilage. In one embodiment, the model represents a human joint afflicted with rheumatoid arthritis.

Abstract: A method of generating a display, or representation, of a simulation model within a graphical user interface (GUI) is described. The simulation model includes a number of objects, which may include state, function, link and modifier objects. The method commences with the display of node representations for at least first and second objects. Thereafter, a link representation, which represents an underlying link object, is selected from a predefined set of link representations to represent a desired relationship condition between the first and second objects. Each link representation of the set is associated with a distinct relationship condition. Each relationship condition may further be defined in terms of an underlying equation. Thereafter, the selected link representation is shown to extend between the respective node representations representing the first and second objects.

Abstract: Methods for predicting the activity of cellular constituents in a biological system are described. In particular, a method for predicting the potential biological activity of a cellular constituent for affecting a biological state is described. A method for identifying biological processes of a biological state modulated by a cellular constituent is also described. Also included is a method for predicting biological processes involved in the action of a drug.

Abstract: An apparatus and method for validating a computer model is described. In one embodiment, a computer-readable medium comprises instructions to associate a set of configurations of a computer model with a stimulus-response test, each configuration of the set of configurations representing a different model scenario, the stimulus-response test defining a modification to each configuration of the set of configurations. The computer-readable medium also comprises instructions to apply the stimulus-response test to the set of configurations to produce a simulated response for each configuration of the set of configurations and instructions to compare the simulated responses for the set of configurations with an expected response to the stimulus-response test.

Abstract: A method of conducting a sequence of linked simulation operations, utilizing a computer-based simulation model, commences with the performance of a first simulation operation to generate an output condition. A further simulation operation, which is defined to sequentially follow the first simulation operation, is then formed utilizing the simulation model. The second simulation operation at least partially and automatically inherits the output condition generated by the first simulation operation as an input condition.

Abstract: A method of managing objects within the simulation model commences with the storage of a first value for a particular parameter within an object of the simulation model. A panel is then displayed within the user interface. The relevant parameter of the above-identified object may then be identified for inclusion within this panel. In response to the identification of the parameter, an identifier (such as an icon) associated with the parameter is displayed within the panel. A second value for the relevant parameter of the object may then be inputted by a user via the panel. The second value for the parameter is then stored separately from the first value for the parameter, and these first and second values can be selectively applied to the parameter.

Abstract: A method of providing access to object parameters of a simulation model involves the display of a diagram panel within a user interface, this diagram panel including icons representative of objects modeled within the simulation model. An access panel is also displayed within the user interface, this access panel being distinct and apart from the diagram panel. A set of object parameters, in terms of which objects within the simulation model may be defined, are identified for inclusion and display within the access panel. In response to identification of the set of object parameters, an identifier for each parameter of the set is displayed within the access panel. A value for at least one of the object parameters is then inputted by a user via the access panel, and this inputted value is then assigned to the relevant parameter.

Abstract: A method of generating a display, or representation, of a simulation model within a graphical user interface (GUI) is described. The simulation model includes a number of objects, which may include state, function, link and modifier objects. The method commences with the display of node representations for at least first and second objects. Thereafter, a link representation, which represents an underlying link object, is selected from a predefined set of link representations to represent a desired relationship condition between the first and second objects. Each link representation of the set is associated with a distinct relationship condition. Each relationship condition may further be defined in terms of an underlying equation. Thereafter, the selected link representation is shown to extend between the respective node representations representing the first and second objects.