A number of other groups have developed methods to determine literature-based functional coherence of gene/protein sets [9], [10], [12], [13], [17].
The goal, criteria, subcriteria (if any), and alternatives can be determined through literature reviews and collective discussions.
The results agree well with the dependence determined from literature values of spherulite growth rate measured by optical microscopy.
Character states were determined from literature and personal observations.
The scaling was determined from literature reviews and comparison between the zooplankton production in warm and cold years (e.g. [33]), which suggest the maximum zooplankton production anomaly is approximately 50% of the mean seasonal zooplankton variability.
Additionally, the specificity of sodC compared to ctrA cannot accurately be determined; the literature does not support the idea that ctrA is the ideal "gold standard" that is needed for a comparison of specificity [11], [12], [40].
Design input requirements were determined following literature specifications.
The functions associated with the various proteins in each subset were then determined by literature searches.
Reversibility of the reactions was determined from literature evidence when available or based on simple thermodynamic considerations [ 52].
A small number of these parameters have been determined from literature which is cited in the revised manuscript.
The expected target pathway for each small molecule was determined from literature and the enzyme database BRENDA.
