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FBA Reaction
Files
An FBA reaction file is a type of single-vector file used to store all of the chemical reactions in a stoichiometric network. The variables in these files are the names (or ID's) of the reactions, and the values are the chemical reactions themselves. The syntax of a line is: The reactants and products are linear combinations of chemical species; they cannot contain any chemical species in common; a chemical species cannot occur more than once on either side of the arrow; the stoichiometric coefficients must be parsable as positive, finite, double precision numbers; and a constant is not allowed. The names of reactions and chemical species cannot contain whitespace or special characters, and chemical species cannot be named "Surroundings" (see below). Reversible and irreversible reactions are denoted with the arrows "<==>" and "-->", respectively. Every reaction in these files is used to create a corresponding column in a stoichiometry matrix S. These files should contain all internal and exchange reactions intended to exist in S. To denote exchange reactions, the word "Surroundings" should appear by itself on one side of the arrow, and a single chemical species should appear on the opposite side. By default, the fluxes of reversible and irreversible internal reactions are constrained to the intervals (-∞, ∞) and [0, ∞), and the fluxes of source, sink, and reversible exchange reactions are constrained to the intervals [0, 0], [0, ∞), and [0, 0], respectively. Additionally, lower flux bounds can never be specified as +∞, upper flux bounds can never be specified as -∞, and lower flux bounds for irreversible reactions can never be assigned a value less than zero. See the FBA Utilities for information about creating and extracting information from these files. See the Text Formatting Rules as well. |