A computerized method of using a data processor having a memory to account for carbon flows and determine a regulatory value for a biofuel can include (i) storing, in memory, a first set of one or more carbon flow values characterizing the production and use of a biofuel derived from a first fraction of an agricultural biomass, (ii) storing, in memory, a second set of one or more carbon flow values characterizing the production and use of a co-product from a second fraction of the agricultural biomass, wherein the second fraction comprises an agricultural residue and wherein the co-product mitigates anthropogenic greenhouse gas emission, and (iii) calculating, using the data processor, a regulatory value for the biofuel from the first and second sets of carbon flow values.