The emerging systems biology paradigm (components -> networks -> computational models -> physiological states) involves two key steps; first, the reconstruction of a network from massive amounts of disparate data, and, second, an assessment of its functional states. We will detail both steps from a bottom-up perspective. The reconstruction process fundamentally the assembly of biochemical, genetic and genomic (BiGG) data in a mathematically structured format: basically the formation of a BiGG knowledge base. The in silico analysis methods that have been developed to compute the functional states of the reconstructed network are fundamentally query tools to interrogate the contents of the BiGG knowledge base.