Systems glycobiology studies the interaction of various pathways that regulate glycan biosynthesis and function. Software tools for the construction and analysis of such pathways are not yet available. We present GNAT, a platform-independent, user-extensible MATLAB-based toolbox that provides an integrated computational environment to construct, manipulate and simulate glycans and their networks. It enables integration of XML-based glycan structure data into SBML (Systems Biology Markup Language) files that describe glycosylation reaction networks. Curation and manipulation of networks is facilitated using class definitions and glycomics database query tools. High quality visualization of networks and their steady-state and dynamic simulation are also supported.