(Molecular) Systems biology has developed over roughly the past 10 years. Its emergence has led to the development of broad genome-wide or network-wide viewpoints of organism functions that have developed against the context of whole genome sequences. Bottom-up approaches to network reconstruction have resulted in organism-specific networks that have a direct genetic and genomic basis. Such networks are now available for a growing number of organisms.

Genome-scale networks have been used to develop constraint-based reconstruction and analysis (COBRA) procedures that treat structural properties of networks, their physiological capabilities, optimal functional states of organisms, and studies of adaptive and long-term evolution. These topics are treated in the companion book that emphasizes that while biology is dynamic, it still functions under the constraints of the topological structure of the molecular networks that underlie its functions.

Events over the time scales associated with distal causation in biology, i.e., over multiple generations, can be studied within the COBRA framework. However, analysis of proximal or immediate dynamic responses of organisms is limited. The recent development of high-throughput technologies and the availability of omics data sets has opened up an alternative approach to building large-scale models that can compute the dynamic states of biological networks. Omics-based abundance measurements (i.e., for proteins, transcripts, and metabolites) can now be mapped onto network reconstructions. In addition, functional states can be determined from fluxomic, exo-metabolomic, and various physiological data types.