cfba_moment_pw: Function: cfba_moment_pw: implement MOMENT method

In sybilccFBA: Cost Constrained Flux Balance Analysis (ccFBA): MetabOlic Modeling with ENzyme kineTics (MOMENT)

Description

This function uses GPR, kcat, and molecular weights to calculate fluxes according to MOMENT method. MOMENT pairwise OR like MATLAB implementation

Usage

cfba_moment_pw(model,mod2=NULL, Kcat,MW=NULL,
selected_rxns=NULL,verboseMode=2,objVal=NULL,
RHS=NULL,solver=SYBIL_SETTINGS("SOLVER"),medval=NULL)

Arguments

model	An object of class modelorg.
mod2	An object of class modelorg with only irreversible reactions. It can be sent to save time of recalculating it with each call.
Kcat	kcat values in unit 1/S. Contains three slots: reaction id,direction(dirxn),value(val)
MW	list of molecular weights of all genes, using function calc_MW, in units g/mol
selected_rxns	optional parameter used to select a set of reactions not all, list of react_id
verboseMode	An integer value indicating the amount of output to stdout: 0: nothing, 1: status messages, 2: like 1 plus with more details, 3: generates files of the LP problem. Default: 2.
RHS	the budget C, for EColi 0.27
objVal	when not null the problem will be to find the minimum budget that give the specified obective value(biomass)
solver	Single character string giving the solver package to use. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTINGS("SOLVER").
medval	median of Kcat values , used for missing values

Details

Main steps 1- Add variables for all genes 2- for each selected reaction: parse gpr, 3- Add variables accordingly and constraints 4-Add solvant constraint

Value

returns a list containing slots: prob:problem object that contains data and model sol: solution of the problem. geneCol: mapping of genes to variables in the problem.

Author(s)

Abdelmoneim Amer Desouki

References

Adadi, R., Volkmer, B., Milo, R., Heinemann, M., & Shlomi, T. (2012). Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters, 8(7). doi:10.1371/journal.pcbi.1002575

See Also

modelorg, optimizeProb

Examples

## Not run: 
	library(sybilccFBA)
	data(iAF1260)
	model= iAF1260
 	data(mw)
 	data(kcat)
 	 mod2=mod2irrev(model)
  
	uppbnd(mod2)[react_id(mod2)=="R_EX_glc_e__b"]=1000
	uppbnd(mod2)[react_id(mod2)=="R_EX_glyc_e__b"]=0
	uppbnd(mod2)[react_id(mod2)=="R_EX_ac_e__b"]=0
	uppbnd(mod2)[react_id(mod2)=="R_EX_o2_e__b"]=1000
	lowbnd(mod2)[react_id(mod2)=="R_ATPM"]=0

  sol=cfba_moment(model,mod2,kcat,MW=mw,verbose=2,RHS=0.27,solver="glpkAPI",medval=3600*22.6) 


## End(Not run)

sybilccFBA documentation built on Dec. 16, 2019, 1:34 a.m.