Creating the Input File

An input file is necessary to specify the system. Normally this is a text file read by the program, although in GUI mode, the input file may be entered directly in the edit window. Several example files are distributed with the program.

This file must contain the differential equations, any other equations specifying relationships between the reactants, the initial reactant concentrations, all reaction rate constants and any other constants necessary. Included among the latter should be the volume occupied by the system, to enable reactant concentrations to be converted to particle numbers. The volume should be given in multiples of litres. The concentration units should be some multiple of molar (mols/litre); the default is $1.0 e^{-9}$ (i.e. if the concentration is listed as 40, that means it is 40 nanomolar), but this may be overridden by a command line or initialisation file option.

The parser ignores blank and comment lines. The latter are indicated by beginning the line with a ``#''

The parser needs some help in establishing the units of each term. Factors in terms which contain a numerator and denominator should have both appear within parentheses. Generally these are factors resulting from the dynamics of the reaction. The user should thus ensure that the product of the rate constant and all remaining unparenthesized reactants has the correct units, which should be some multiple of molar per second. However, if the input is correct and each factor has the correct units, this should be achieved automatically.

Although the order of individual lines in the file is irrelevant, it is vital to use the correct type of assignment operator ($=$, $:=$, $-\!\!\!>$etc.) on each line. The symbol $=$ is used for differential equations, other equations and constant assignment. The symbol $:=$ is used for assigning the cell volume. The symbol $-\!\!\!>$is used to assign the values of the rate constants.

Important to note is that constants which should have the same units as reactants should be entered as reactants. For example, the constant $K_m$ in Michaelis-Menten kinetics, although derived in terms of the more fundamental reaction rates, should be have its value assigned with the equality sign used to assign reactants. This is easily understood if one notes that it appears in terms such as $[S] / \left( K_m + [S] \right)$, and thus should scale like the reactant $[S]$. The reason for this (possibly confusing) situation is that although the differential equations are expressed in terms of reactant concentrations, the simulation is performed using actual particle numbers.

A common source of error is input files which are incomplete or wrong. You should make sure that all variables and constants in the differential equations are given values or initialised, once and only once. Make sure also that the values you give make physical sense, e.g. the concentrations should not be so low that no particle number is greater than zero.

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