given Kcat vector (in 1/Sec), and molecular weights and optionally protein complex stoichiometry formulate a ccFBA problem(Maximize biomass). Improvements over MOMENT: 1- use multifunctioning enzyme constraint. 2-use one enzyme (the cheapest) for each reaction catalayzed my multiple isoenzymes and thus eliminate under estimation of rules of form ((A AND B) OR (A AND C)) 3-optionally include protein complex stoichiometry
getccFBA_mat(model, mod2 = NULL, Kcat, MW = NULL, selected_rxns = NULL, verboseMode = 2,
objVal = NULL, RHS = NULL, solver = SYBIL_SETTINGS("SOLVER"), medval = NULL,
cpx_stoich = NULL, C_mu_coef = 0)An object of class modelorg.
An object of class modelorg with only irreversible reactions.
It can be sent to save time of recalculating it with each call.
kcat values in unit 1/S. Contains three slots: reaction id,direction(dirxn),value(val)
list of molecular weights of all genes, using function calc_MW, in units g/mol
optional parameter used to select a set of reactions not all, list of react_id
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.
the budget C, for EColi 0.27
when not null the problem will be to find the minimum budget that give the specified objective value(biomass)
Single character string giving the solver package to use. See
SYBIL_SETTINGS for possible values.
Default: SYBIL_SETTINGS("SOLVER").
median of Kcat values , used for missing values
giving the stoichiometry of complexes: data frame containing at least two columns 'genes','stoich' 'gene' : delimited string of genes(ordered by geneid(e.g bnumber)), 'stoich': number of subunits of each gene in the same order in 'genes' Default: NULL (e.g. all stoichiometry coefficients equal one)
used to have C as a linear function of mu (biomass) : C = RHS + C_mu_coef*Biomass default 0 (e.g. ignored).
return a LIST,
constraint matrix, consists of S matrix and ccFBA constraints
bounds for constraints (i.e rows)
bounds for variables (i.e columns)
mapping of Kcat values to constraints
complex stoichiometry as returned by getGpr1iso
rxn_id,gene,Col : used to get MCrowding
low level structure, used for debugging
row index of constraint on FBA model objective
capacity constraint index
variable names: g1_x_1: indicates that gene x is in one-to-one relation gr_x_r:indicates that gene x catalyzes more than one reaction and this variable is the portion that catalyzes reaction r. gmr_x_cnt: variable for a gene catalyzing more than one reaction (i.e cnt reactions) and this variable is the sum of individual parts. cpx_r: used to represent a complex catalyzing reaction r.
Desouki, Abdelmoneim. "Algorithms for improving the predictive power of flux balance analysis." PhD diss., 2016.