sybilccFBA (version 3.0.1)

cfba_moment_pw: Function: cfba_moment_pw: implement MOMENT method

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

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.

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

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) 

# }
# NOT RUN {
<!-- % end dontrun -->
# }