Abstract: The present invention relates to a method and system for automatically constructing computer simulation models of biological systems. More specifically, a series of simulation models are created, or selected from a repository of standard models, preferably based on experimental data. These models are then calibrated, if necessary, based upon experimental data and then compared to each other for goodness of fit to a set of experimental data; the best models can then be selected based upon the goodness-of-fit calculations. Another aspect of the invention provides for automated design of additional experiments to differentiate between models that have the same or similar goodness-of-fit scores.

Abstract: The present invention relates to a method and system for quantitative and semi-quantitative modeling of biological and physiological systems using image data. More specifically, the system utilizes time-series image data to improve the accuracy of the predictions made by a simulation model capable of forecasting the spatiotemporal evolution of a given biological or physiological system. Furthermore, in accordance with another aspect of the invention, the quality of experimentally acquired images can be improved by using a simulation model to eliminate noise and measurement errors from the acquired image data. Finally, in accordance with another aspect of the invention, certain undamped random disturbances in a biological or physiological system can be detected and tracked by applying a fading-memory filter to acquired time-series data and predictions of the time series using a simulation model that takes into account underlying physiological, chemical or biological variables.

Abstract: The present invention relates to a system and method for modeling a biological system. More specifically, the present invention relates to the use of a component-based architecture for biological modeling software, thereby enhancing the extensibility of the software and the reusability of the software components. The present invention also relates to the use of distributed components for constructing biological modeling software capable of being run in a distributed computing environment. Also provided are computer program products for implementing such methods and systems.

Abstract: The present invention relates to a method and system for quantitative and semi-quantitative modeling of biological and physiological systems. More specifically, the invention relates to the use of overlays to store and manipulate computational biological models. Also provided by the invention are methods and systems for preparing overlays, methods and systems for creating new computational biological models by applying overlays to old models, and computer program products comprising overlays.