Constraint-based methods to analyse metabolic
networks require the classification of metabolites
into external compounds that are exchanged with
the system environment, and internal ones that
form intermediate steps on the metabolic pathways
and which are therefore subject to stoichiometry
constraints in the steady state.
For eukaryotic cells it is not practical to analyse
the complete cellular network, and so the
subnetwork that describes the specific phenomena
under study needs to be extracted. This study
focuses on flavonoid production in the model
plant Arabidopsis Thaliana.
Software was developed to extract the full
Arabidopsis metabolic network from the AraCyc
database, in a format required by standard network
analysis packages. Considerable processing is also
required to reconcile information about reaction
directions from different database tables and to
classify metabolites as internal or external to the
subnetwork. The paper outlines the strategies
implemented in the software to address these
issues.[Show full abstract]
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