Anaerobic digesters (AD) have different requirements when hog manure is used instead of dairy manure. As well, chemicals like antibiotics and disinfectants can impede the AD functioning. Some level of inhibiting substances, like ammonia, is normal, but if these levels get too high the AD will stop. The maximum level of inhibiting substances an AD can tolerate will depend on the individual substrate and microorganisms. Mathematical simulations can be run to predict yield and stability under various conditions, and a program known as Aquasim has been developed to do so. Aquasim has been run to determine Biochemical Methane Potential with different substrates, to create a semi-continuous flow model for bioethanol by-product, and to monitor a stable dairy biogas plant. The program can fairly accurately predict the complex biological and chemical response of an anaerobic digester under multiple conditions.