Abstract: The invention relates to a federated patient-centric database which is modular and disease agnostic.

Abstract: A digital computer system stratifies in a set of patients, based on a set of observations. The observations can include physical, biochemical, histological, genetic, and gene-expression data, among other types of information. Adjustments can be made to account for the possibility that observations of several patients may begin at different points in the progression of their respective disease processes. Once these adjustments are made, the data are subjected to a statistical cluster analysis. Each cluster of patients potentially represents a different disease stratum, with its own underlying cause, optimum therapy, and prognosis. Once the strata are defined and patients are assigned to them, adjustments to the data can be refined. The cluster analysis then can be repeated, and so an iterative process of stratification and staging takes place.

Abstract: A method of evaluating a biochemical pathways models using clinical data, includes representing the biological model within a computing system, in the form of a hierarchy of Petri nets or stochastic activity nets, wherein the nodes of the net represent biological or biochemical components, and the arcs correspond to the flow of biochemical components in the model. A time series of measurements of some of the biochemical components described by the model are recorded and an observed pattern of relationships between inputs and outputs of the respective nodes is compared to an expected pattern of the relationships to determine whether the model describes the behavior of the biochemical components.