Table 1.

Summary of modules and their usage.

Module name	Description	Parameters	Potential usage
FaceCon
Coupling module	Module allows researcher to enforce weak or directional coupling. To enforce only weak coupling a second sub-problem is added	vmin, δa, σa	Can be used to define the nature of coupling proposed by metabolic engineering algorithms. Can be useful when proposals tend to generate sickly mutants
Chemical level module	Module allows researchers to define minimal or maximal chemical production limits, β, beyond a user defined point vmin	vmin, β	Can be used to eliminate undesired by-products or to define minimal chemical production criteria
Direct constraint module	Module allows researchers to create an exclusion region of their own design, defined by the line going through the point (α,γ) with the slope mset	vmin, α, γ, mset	Can be used to propose co-production or co-utilization of metabolites. All FaceCon modules are special cases of the direct constraint module
Other
ShadowCon module	Module allows greater control over the degree of coupling once it has initiated	mmin, mmax	Can be used to vary the intensity of selective pressure on a reaction when coupled to growth rate

^aParameters are only used when additional module sub-problems are required (e.g., when only weakly coupled mutants are desired).