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Bio‐based products and fuels are produced from renewable biomass sources such as conventional food crops and dedicated energy crops, forestry products, and organic residues (Langeveld et al., 2010). Bio‐based systems refer to those producing non‐food bio‐products and biofuels, and they consist of the biomass production and conversion processes. Bio‐products include a wide variety of products from those with low value and high volume, such as glycerin and lactic acid, to those with high value and low volume, such as those used in food or pharmaceuticals industries (Langeveld et al., 2010). Biofuels include gas, liquid, or solid fuel types produced directly or indirectly from biomass. The bio‐based systems in this book chapter refer to those which are used to produce agricultural crop‐based biofuels.