Flux Balance Analysis

Performs basic flux balance analysis (fba)

Usage

fba(model)

Arguments

model

Model of class ModelOrg

Value

A list with flux predictions (reaction fluxes 'fluxes', reduced costs 'redCosts'), and optimization status ()

See also

Other Flux prediction algorithms: fva(), pfba(), pfbaHeuristic()

Examples

fpath <- system.file("extdata", "e_coli_core.xml", package="cobrar")
mod <- readSBMLmod(fpath)

# aerobic growth
res_aero <- fba(mod)
cat(" Growth rate:       ", res_aero@obj,"\n",
    "Acetate production:", res_aero@fluxes[mod@react_id == "EX_ac_e"],"\n")
#>  Growth rate:        0.8739215 
#>  Acetate production: 0 

mod <- changeBounds(mod, react = "EX_o2_e", lb = 0) # before: -1000
res_anaero <- fba(mod)
cat(" Growth rate:       ", res_anaero@obj,"\n",
    "Acetate production:", res_anaero@fluxes[mod@react_id == "EX_ac_e"],"\n")
#>  Growth rate:        0.2116629 
#>  Acetate production: 8.503585