Definitions of Terms:

Computational Prediction – Type of constraint-based modeling prediction used:

• Flux Phenotype – Calculation of metabolic fluxes, nutrient uptake, or growth rate
• Essentiality (Global) – Untargeted screen of knockouts
• Knockout (KO, Targeted) – Targeted growth of select mutants or rational selection of knockouts
• Thermodynamics – Modeling incorporates or makes predictions on thermodynamics of reactions
• Objective function – Modeling and analysis to determine objective function
• System-scale property – Determines global property of metabolic network
• Metabolite phenotype – Modeling and analysis for determining properties of metabolites in network
• Macromolecular interaction phenotype – Integrates interaction networks (e.g. transcriptional regulation, genetic interactions) or uses metabolic network to analyze such networks
• Synthetic biology – Incorporates novel pathways into metabolism
• Biological discovery – Uses model to extend or refine biochemical knowledge
• Experimental Design (ExpDes) – Modeling analysis is used to design new experiments
• Pathway Analysis – Utilizes Extreme Pathways or Elementary Flux Modes and their derivatives
• Other Phenotype – miscellaneous

High-throughput data integration – Type of high-throughput data integrated with modeling for predictions

Prediction Application – General field that predictions are used for:

• General biological sciences –
• Met Eng – metabolic engineering
• Inf – infectious disease
• Env – environmental
• Biomed – biomedical sciences

Consistent with experiments – computational predictions are compared to experimental data:

• Legacy data – consistent with experiments in previous publications
• Prospective experimental validation – experiments are performed in the publication