sybilDynFBA (version 1.0.2)

sybilDynFBA-package: Dynamic Flux Balance Analysis

Description

The package sybilDynFBA implements dynamic flux balance analysis as proposed by Varma et al (1994). It uses functions from package sybil to find standard FBA solution. Solution can also be plotted.

Details

Package:	sybilDynFBA
Type:	Package
Version:	1.0.0
Date:	2015-07-24
License:	GPL Version 3
LazyLoad:	yes
Depends:	sybil

References

Varma, A. and Palsson, B.O. 1994. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 60: 3724-3731.

See Also

sybil

Examples

# NOT RUN {
	## The examples here require the package glpkAPI to be
	## installed. If that package is not available, you have to set
	## the argument 'solver' (the default is: solver = "glpk").

	## load the example data set
	data(Ec_core)
    mod <- Ec_core

    # Change bounds for glucsoe, oxygen and acetate uptake
    mod <- changeBounds(mod, react = "EX_glc(e)", lb = -12)
    mod <- changeBounds(mod, react = "EX_o2(e)",  lb = -10)
    mod <- changeBounds(mod, react = "EX_ac(e)",  lb = -10)

    # initial values
    init.source <- c("EX_ac(e)","EX_o2(e)","EX_glc(e)")
    init.conc   <- c(10,50,28)
    init.bmass  <- 0.01

    # dFBA
    Ec_df <- dynamicFBA(mod,exclUptakeRxns = c(),
                        substrateRxns      = init.source,
                        initConcentrations = init.conc,
                        initBiomass        = init.bmass,
                        timeStep=.1,nSteps=200,verbose=3)


    # Plotting
    plot(Ec_df,
      plotRxns=c('EX_glc(e)','EX_ac(e)',"EX_for(e)","EX_o2(e)"),
                      legend_cex=0.85,legend_xpos=0,legend_ypos=45)

# }