makeModel: Creating a model

In Vessy/sysBio: A package for modeling biological systems

Description

This function creates mathematical model of the system, a set of differential equations that correspond to that mathematical model, stochastic matrix, and propensity function. It also transforms all defined rates, parameters, and rules into a format required by the ODEs solver function.

Usage

makeModel(x)

Arguments

x	model name (required)

Value

This function adds updates model (given as an argument of the function) with information about mathematical model of the system, ODEs, stochastic matrix, and propensity function. This function also updates model's isChecked flag, as model is created based on the most recent data. It updates the following elements:

• model - mathematical model of the system

• odes$equations - a set of ODEs that correspond to the mathematical model of the system (in format for ODEs solver)

• odes$rates - reaction rates assignments (in format for ODEs solver)

• odes$parameters - parameters assignments (in format for ODEs solver)

• odes$rules - rules assignments (in format for ODEs solver)

• stochMatrix - stochastic matrix (rows correspond to species, columns to reactions)

• stochModel - propensity function (one equation for each reaction)

• isChecked - flag set to 1

Examples

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")

addMAreactRate(exmp, "rf", "fixed", "1")
addMAreactRate(exmp, "rb", "fixed", "0.75")
addMAreactRate(exmp, "k", "fixed", "0.5")
addMAreactRate(exmp, "rAB", "assigned", "p1*A")

addParameters(exmp, "p1", 0.75)
 
addSpecies(exmp, "A", 10)
addSpecies(exmp, "B", 10)
addSpecies(exmp, "AB", 0)

addRule(exmp, "rule B", "ODEs", "B=-0.1*AB")

# Show info about the model
exmp

makeModel(exmp)
  
# Show info about the updated model
exmp

Vessy/sysBio documentation built on May 9, 2019, 9:55 p.m.