Suddenly, systems biology is everywhere. What is it? How did it arise? The driving force for its growth is high-throughput (HT) technologies that allow us to enumerate biological components on a large scale. The delineation of the chemical interactions of these components gives rise to reconstructed biochemical reaction networks that underlie various cellular functions. Systems biology is thus not necessarily focused on the components themselves, but on the nature of the links that connect them and the functional states of the networks that result from the assembly of all such links. The stoichiometric matrix represents such links mathematically based on the underlying chemistry, and the properties of this matrix are key to determining the functional states of the biochemical reaction networks that it represents.

The Need for Systems Analysis in Biology

Biological parts lists

During the latter half of the 20th century, biology was strongly influenced by reductionist approaches that focused on the generation of information about individual cellular components, their chemical composition, and often their biological functions. Over the past decade, this process has been greatly accelerated with the emergence of genomics. We now have entire DNA sequences for a growing number of organisms, and we are continually delineating their gene portfolios. Although functional assignment to these genes is presently incomplete, we can expect that we will eventually have assigned and verified function for the majority of genes on selected genomes.