In 1995, the first full genome sequence became available, ushering in the genome era. Since then, a large number of high-throughput technologies have enabled us to define the molecular parts catalogs of cellular components. Although these catalogs are still incomplete, it is now possible to reconstruct, based on this and other information, genome-scale networks of biochemical reactions that take place inside cells. This process of network reconstruction, followed by the synthesis of in silico models describing their functionalities, is the essence of systems biology.

The functions of reconstructed networks are defined by the interconnections of their parts. Since these connections involve chemical reactions, they can be described by a stoichiometric relationship. The stoichiometric matrix, which contains all such relationships in a network, is thus a concise mathematical representation of reconstructed networks. This matrix comprise integers that represent time- and condition-invariant properties of a network. It may therefore be expected to represent a key in the study of the functionalities of complex biochemical reaction networks. Its content and associated information effectively constitute a biochemically, genetically, and genomically structured database.

This book is focused on the stoichiometric matrix. In order to satisfactorily understand the material, good knowledge of linear algebra and of biochemistry is needed. Most of the mathematical concepts and principles, when properly interpreted, have a direct biological and chemical meaning. This text thus tries to relate what might be seen as abstract mathematical quantities to real biological and chemical features.