The main disease areas of study are metabolic diseases like diabetes and obesity as well as neurodegenerative diseases with main focus on Alzheimer's. We adopt a systems approach to omics data analysis - based on multivariate statistical and network analysis - to generate biologically interpretable results from hierarchical, multi-source data sets to identify functional modules in large network models. These functional modules represent a first step towards quantitative, mechanistic understanding of disease-linked system components, and response to external/environmental components (i.e., drugs or food). Quantitative models derived from functional modules are then simulated to gain new insight on the biological behavior. Simulation techniques are based on stochastic, hybrid and deterministic algorithms, which can be analysed for sensitivity of parameters as well.