  The large-scale shape and function of metabolic networks are intriguing
topics of systems biology. Such networks are on one hand commonly regarded as
modular (i.e. built by a number of relatively independent subsystems), but on
the other hand they are robust in a way not expected of a purely modular
system. To address this question we carefully discuss the partition of
metabolic networks into subnetworks. The practice of preprocessing such
networks by removing the most abundant substrates, "currency metabolites," is
formalized into a network-based algorithm. We study partitions for metabolic
networks of many organisms and find cores of currency metabolites and modular
peripheries of what we call "commodity metabolites." The networks are found to
be more modular than random networks but far from perfectly divisible into
modules. We argue that cross-modular edges are the key for the robustness of
metabolism.
