  This paper addresses the problem of model reduction for dynamical system
models that describe biochemical reaction networks. Inherent in such models are
properties such as stability, positivity and network structure. Ideally these
properties should be preserved by model reduction procedures, although
traditional projection based approaches struggle to do this. We propose a
projection based model reduction algorithm which uses generalised block
diagonal Gramians to preserve structure and positivity. Two algorithms are
presented, one provides more accurate reduced order models, the second provides
easier to simulate reduced order models. The results are illustrated through
numerical examples.
