Description Details Author(s) References See Also Examples
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.
Package: | sybilDynFBA |
Type: | Package |
Version: | 1.0.0 |
Date: | 2015-07-24 |
License: | GPL Version 3 |
LazyLoad: | yes |
Depends: | sybil |
Abdelmoneim Amer Desouki
Maintainer: Abdelmoneim Amer Desouki <abdelmoneim.amer@uni-duesseldorf.de>
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | ## 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)
## End(Not run)
|
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