TECHNOLOGY FOCUS - ELECTRICAL POWER AND ENERGY - Preferred Function: A portion of the hydrogen-containing gas is used in electrical energy production, mechanical energy production, thermal energy production, and/or chemical synthesis. The electrical energy is produced by combusting the hydrogen-containing gas in a gas turbine, an internal combustion engine, and/or a fuel cell. A portion of the hydrogen-containing gas is used in a boiler to produce steam. The steam is further used in power production in a steam turbine, and/or process steam applications.    TECHNOLOGY FOCUS - ORGANIC CHEMISTRY - Preferred Method: The method further comprises enriching the hydrogen-containing gas in hydrogen content by separating a hydrogen component with a membrane, preferentially removing non-hydrogen content, or subjecting the hydrogen-containing gas to a water gas shift reaction; processing the hydrogen-containing gas in an acid gas removal unit, so as to produce hydrogen sulfide gas as a byproduct; separating carbon dioxide from the hydrogen-containing gas; using the separated carbon dioxide in the step of extracting oil from the bio-oil feedstock; directing the hydrogen-containing gas to a Fischer Tropsch synthesis reaction, to produce additional amounts of a fuel composition; preparing a slurry of the deoiled residue with at least a portion of the light hydrocarbon, prior to the gasification step; and reforming a portion of the fuel composition to generate a hydrogen-containing gas, where a portion of the hydrogen-containing gas is consumed in upgrading the bio-oil. The step of upgrading the bio-oil further comprises sequential steps of hydro-treating, hydro-isomerization, and separation. A portion of the hydrogen sulfide gas produced in the acid gas removal unit is brought into contact with a hydro-treating catalyst which is present in the bio-oil upgrading step, so as to substantially maintain or increase the activity of the catalyst. A portion of the light hydrocarbon is used in the step of extracting oil from the bio-oil feedstock, as a solvent extraction medium. The step of upgrading the bio-oil produces a light hydrocarbon byproduct. A portion of the light hydrocarbon byproduct is used in the gasification of the deoiled residue to reduce tar formation. A portion of the energy produced by the hydrogen-containing gas is employed to carry out the step of upgrading the bio-oil. Preferred Component: The bio-oil comprises fatty acids. The bio-oil feedstock comprises palm; coconut; corn; cottonseed; algae; and/or oilseeds comprising soy, camelina, mustard, sunflower, and/or jatropha. EXAMPLE - A soybean material (8170 tons per day (tpd)), used as a bio-oil feedstock, was subjected to oil extraction to produce bio-oil (10000 barrels per day (bpd)) and deoiled residue (40). The deoiled residue was separated into components comprising lecithin (245 tpd), hulls (817 tpd), and protein meals (5637 tpd) and directed to a boiler that used water to produce steam. A portion of the deoiled residue comprising lecithin (46 tpd) was sent to gasification island to produce hydrogen-containing gas (4.5 wt.% hydrogen) used in oil upgrading process comprising hydro-treating, hydro-isomerization, and separation. The hydro-isomerization step produced a mixture of liquefied petroleum gas (butane) (5%), naphtha and gasoline (20%), Jet fuel (40%), and diesel fuel (35%). Jet fuel (6000 bpd) and light hydrocarbons (butane, naphtha and gasoline) were separated.