The resultant specification of reactions and chemical entities enables simple, yet powerful SPARQL-based queries, e.g. to find the potential reactions of a given molecule and identify the atoms and functional group instances involved in these reactions (Appendix 11).
Within this display, reactions can be selected, prompting the NetworkViewer to visually indicate the particular states the participating complexes are in when the reactions occur and what their resulting states are, thus providing complete specifications of reaction rules embedded into network maps.
Although this approach allows for the detection of general electrogenic oxidation activity, it does not allow for specification of the anodic reaction involved.
The command line interface additionally allows the independent specification of new tailoring reactions to add to the original scaffold, tailoring reactions to remove from the original scaffold, and tailoring reactions whose sites may be changed.
A biochemical model is fully characterised by the initial concentration of each molecular species and the specifications of the reactions with their kinetic rate laws.
For the specification of metabolic and isotopic reaction networks, the XML-based document format FluxML has been developed.
Additional constraints that can be modeled in the FBA include specification of reversible and irreversible reactions, as well as limits placed on substrate uptake and target reaction rates.
Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites.
Finally, the characterization of the cetyl ricinoleate obtained in the vacuum reactor demonstrated that the product obtained after only 3 or 4 h of reaction meets manufacturers' specifications.
