dynamicFBA: dynamic flux balance analysis

In sybilDynFBA: Dynamic FBA : Dynamic Flux Balance Analysis

Description

Calculate concentrations of metabolites of exchange reactions at defined time points given the initial concentrations. To accomplish this task this function calls optimizeProb function to get the fluxes then update the concentrations and the reaction boundaries ..etc.

Usage

dynamicFBA(model, substrateRxns, initConcentrations, initBiomass, timeStep, nSteps, 
	exclUptakeRxns, 
	retOptSol = TRUE,
 fld = FALSE, verboseMode = 2, ...)

Arguments

model	An object of class modelorg.
substrateRxns	List of exchange reaction names for substrates initially in the media that may change (e.g. not h2o or co2)
initConcentrations	The given start concentrations of substrates
initBiomass	The start value of biomass (must be nonzero)
timeStep	Define the points of time to evaluate the problem at.
nSteps	The maximum number of steps, the procedure may stop before completing this number when the substrate run out.
exclUptakeRxns	List of uptake reactions whose substrate concentrations do not change (Default ='EX_co2(e)','EX_o2(e)','EX_h2o(e)','EX_h(e)')
retOptSol	Boolean. indicates if optsol calss will be returned or simple list. Default: TRUE
fld	Boolean. Save the resulting flux distribution. Default: FALSE
verboseMode	An integer value indicating the amount of output to stdout: 0: nothing, 1: status messages, 2: like 1 plus a progress indicator, 3: a table containing the reaction id's and the corresponding min max values. Default: 2.
...	Further arguments passed to sysBiolAlg. Argument solverParm is a good candidate.

Value

returns optsol_dynamicFBA

Author(s)

Abdelmoneim Amer Desouki

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.

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2, 727–738.

See Also

modelorg, optsol_dynamicFBA, optimizeProb, sysBiolAlg, SYBIL_SETTINGS

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)
        lowbnd(Ec_core)[react_id(Ec_core)=='EX_glc(e)']=-10;
        lowbnd(Ec_core)[react_id(Ec_core)=='EX_o2(e)']=-18;
	## run dynamicFBA(), Ec_df will be an object of class \code{\link{optsol_dynamicFBA}}
	Ec_df <- dynamicFBA(Ec_core,substrateRxns={'EX_glc(e)'},initConcentrations=10,
		initBiomass=.035,timeStep=.25,nSteps=20,verbose=3)

	## plot biomass and reactions
	plot(Ec_df,plotRxns=c('EX_glc(e)','EX_ac(e)'));


## End(Not run)

Example output

Loading required package: sybil
Loading required package: Matrix
Loading required package: lattice
[1] "Default extra cellular uptake reactions will be used: "
[1] "EX_co2(e)" "EX_o2(e)"  "EX_h2o(e)" "EX_h(e)"  
Loading required package: glpkAPI
using GLPK version 4.65
[1] "Step number    Biomass\n"
[1] "1    0.0426072245959749"
[1] "2    0.0518678739363399"
[1] "3    0.0631413186891815"
[1] "4    0.0768650384764591"
[1] "5    0.0935715987984213"
[1] "6    0.113909317880252"
[1] "7    0.138667425442811"
[1] "8    0.168806689713928"
[1] "9    0.205496701198414"
[1] "10    0.250161260048371"
[1] "11    0.304533628345526"
[1] "12    0.370723791427001"
[1] "13    0.451300338411486"
[1] "14    0.549390139398223"
[1] "15    0.668799687432989"
[1] "16    0.732619669578131"
[1] "17    0.749656881403476"
[1] "No feasible solution - nutrients exhausted\n"

sybilDynFBA documentation built on July 1, 2020, 6:07 p.m.