Subsystems provide a natural framework for comparative genome analysis and functional annotation. A subsystem may be implemented in a number of different functional variants in individual species.  ...  However, no computational techniques are presently available for an automated detection and analysis of subsystem variants.  ...  Daugherty who directly contributed to the early bioinformatics and experimental analysis of these subsystems. We thank Dr R. Edwards for providing feedback on the manuscript.  ... 

The analysis of the dynamic behaviour of genome-scale models of metabolism (GEMs) currently presents considerable challenges because of the difficulties of simulating such large and complex networks.  ...  This enables the generation of abstract views of the behaviour of these models, which can be large-up to whole genome in size-and therefore impractical to analyse informally by eye.  ...  We demonstrate the use of our techniques to explore model behaviours under different growth conditions, with a focus on the reaction perspective related to functionally meaningful subsystems (pathways)  ...