Table 2.

Criteria for removal of reactions from enforce/suppress sets

Rule	Reaction type	Issue
1	Dead-end	Subnetworks cannot evenly distribute EFMs
2	Reversible	Misses EFMs containing flux in either but not both directions
3	Combineda	May not allow for all reaction combinations
4	Poorly scaled coefficients	Poorly conditioned matrix and zero definition may miss EFMs (threshold difference of 10)

Note: All reaction combinations must be tested to confirm that an EFM is not represented in the enforce/suppress set and that the subnetwork definition and compression does not rearrange reactions causing violation of the stated rules. ^aSee Section 3.1 for detailed description of combined reactions to avoid.