TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preferred System: In (I), the biomass is lignocellulosic biomass chosen from bagasse and corn stover. The gravel layer is approximately three feet thick. The lime input device is operable to deliver lime to the biomass either during or after the delivering of the biomass over the gravel layer in an amount between approximately 10% and 30% of the biomass by weight. (I) further has an inoculum input device (120) operable to deliver an inoculum to the biomass pile for fermentation of the biomass pile, a heat exchanger (128) coupled to the distribution pipe and operable to control a temperature of the water that is delivered to the distribution pipe, an air blower (124) and an air distribution pipe operable to deliver air to the biomass pile, container (126) of lime water slurry coupled to the air distribution pipe and operable to scrub the air of carbon dioxide before the air is delivered to the biomass pile, a calcium carbonate input device operable to deliver calcium carbonate to the biomass for pretreating the biomass. (I)-(b) further has a sugar extraction device operable to extract sugar from a raw feedstock to produce the biomass. The raw feedstock is chosen from energy cane and sweet sorghum. The sugar extraction device several of adjacent extraction tanks, each extraction tank comprising, a screw conveyor operable to deliver solid material from the raw feedstock in a downstream direction, and a weir operable to deliver liquid material from the raw feedstock in an upstream direction. In (I)-(d), each of the top liner comprises several of hexogonal or pentagonal panels coupled to one another with lips associated with each panel.Preferred Method: (M1) further involves incubating the mixture for a time period of at least approximately 4-16 weeks, selecting the duration of incubation based on incubation temperature. The biomass comprises lignocellulosic biomass or agricultural waste. The biomass is chosen from bagasse, corn stover and their combinations. (M1) further involves circulating water and oxygen enriched air through the biomass during incubation. The alkali comprises lime, preferably calcium oxide. (M1) further involves adding approximately 0.5 g, preferably 0.1-0.5 g of lime/g of biomass, in an amount between approximately 10% and 30% of biomass by weight, to produce the mixture. (M1) further involves incubating the mixture at a temperature between approximately 25 degrees C and 90 degrees C, preferably 25 degrees C and 57 degrees C, selecting the incubation temperature based on the partial pressure of water at the selected temperature, increasing the enzyme digestibility of the biomass, producing pulp suitable for paper or cardboard production and reducing the lignin content of the biomass by at least approximately 98%, 90%, 29%, 40%, or 67%. The lignin content is reduced by alkaline oxidation. (M1) further involves fermenting the biomass after incubation, adding an inoculum to the mixture after incubation, collecting carboxylate salts from the mixture, placing the mixture prior to incubation in a storage facility suitable for incubation and fermentation. (M2) and (M3) further involves circulating air through the mixture during incubation. (M2) further involves reducing the lignin content of the biomass by at least approximately 67% or 32% and fermenting the biomass after incubation. (M3) further involves reducing the lignin content of the biomass by at least approximately 90% or 40% and producing paper or cardboard from the biomass after incubation.