Overview of the network model definition text file. The model definition file consists of one table and five lists. The metabolic reaction network is defined in the table, and is organized under the following headings: reaction ID (rxnID), reaction equation (rxnEQ), reaction atom transition (rxnCTrans), reaction rate (rates), reaction type (rxnType), free flux allocation (basis) and flux value standard error (deviation). If a given reaction rate is known (e.g., biomass drain rates), then the flux value and the corresponding measurement error can be included in the basis and deviation columns respectively. The parser requires the user to separately list down metabolites that are excluded from the stoichiometric model (excludedMetabolites), EMUs that are to be calculated by the isotopomer model (simulatedMDVs), and input substrates that contribute to the isotopomer balance (inputSubstrates). The experimental MIDs (measurements) and the associated errors (error) are listed in the same order as the EMUs in the simulatedMDVs list. The figure insert (bottom right) is an example of how pyruvate dehyrogenase reaction is described in the rxnEQ and rxnCTrans columns. CO2 is produced by cleaving the carboxylic end (C1) of pyruvate, leaving the acetyl moiety (C2–C3). Alphabet letters in the atom transition equation is used to represent the transfer of first carbon atom of pyruvate to CO2, and the second and third atoms of pyruvate to the first and second atoms of acetyl moiety. An exception is the letter "x" or "X", which is used to exclude metabolite from the isotopomer balance, such as NADH.