addMAreaction: Adding molecular reactions.
In Vessy/sysBio: A package for modeling biological systems

Description Usage Arguments Value Examples

Molecular reactions can be described by differential equation that define the rate of change in molecular concentrations. addMAreaction function transforms reactions into ODEs using the law of mass action. Given a reaction: k1A + k2B -(r)-> k3*AB, where A and B represent reactants and AB represents a product (in general, we can call A, B, and AB species), r represents the reaction rate, and k1, k2, and k3 represent stoichometric coefficients, one can use the law of mass action to determine the change in the amount of each species as: dA/dt = dB/dt = - dAB/dt = -rA^(k1)B^(k2). Or in general, given a reaction sum(i=1:m)[kiSi] -(r)-> sum(j=1:n)[ljSj], changes in the amount of each species can be represented as dS/dt = r(li-ki)prod(i=1:m)S^(ki). addMAreaction function adds a mass action reaction into an existing model. sysBio allows users to write reactions in two formats: 1. as forward (non-reversible) reactions, e.g., A -> B, with rate r, 2. as reversible reactions, e.g., A = B, with forward rate r1 and reverse rate r2. sysBio transforms and interprets the reversible reactions as two forward reactions, e.g., A -> B, with rate r1, and B -> A, with rate r2.

1 2	addMAreaction(x, react = NA, r1 = NA, r2 = NA, name = NA, overwrite = FALSE)

`x`	model to which the reaction is added (required)
`react`	reaction to be added (required). sysBio uses the "->" symbol for forward reaction and the "=" symbol for the reversible reaction; values that represent stoichometric coefficients should be explicitly included in the reaction definition (e.g., 2A + B -> 1.5AB); sysBio uses a term null to describe a null species (source or sink).
`r1`	reaction rate (forward); if the name is not specified, sysBio will assign a generic name to the reaction rate, in the format r_reaction_rate_number
`r2`	reaction rate (reversible); if the name is not specified, sysBio will assign a generic name to the reaction rate, in the format r_reaction_rate_number
`name`	name of the reaction; if the name is not specified, sysBio will assign a generic name to the reaction, in the format Reaction_reaction_number
`overwrite`	a flag that allows changes to the existing reaction (default value FALSE)

This function adds information about the reaction into the model (given as a first argument of the function). Reaction information is stored in the list format and contain the following elements:

reaction$rName - name of the reaction
reaction$reaction - reaction
reaction$r1 - forward rate of the reaction
reaction$r2 - reverse rate of the reaction (if available, NULL otherwise)
reaction$type - asigned type "Mass Action"

exmp <- newModel("This is an example of a new model")
addMAreaction(exmp, react="A = null", "rf", "rb")
addMAreaction(exmp, react="A + B -> 2*AB", "k", name="Forward AB")
addMAreaction(exmp, react="AB -> null", "rAB")

# Show info about model reactions
exmp$reaction