sybil (version 1.1.2)

addExchReact: Add Exchange Reactions to a Model

Description

The function addExchReact adds exchange reactions for a set of metabolites to a metabolic model.

Usage

addExchReact(model, met, lb, ub)

Arguments

model

An object of class modelorg.

met

A vector of character strings containing the metabolite id's to add exchange reactions for.

lb

A vector of numeric values of the same length as met containing the lower bounds for the exchange reactions. Default: rep(0, length(met)).

ub

A vector of numeric values of the same length as met containing the upper bounds for the exchange reactions. Default: rep(SYBIL_SETTINGS("MAXIMUM"), length(met)).

Value

• An object of class modelorg

encoding

utf8

Details

If lb[i] < 0, the exchange reaction for the metabolite in met[i] is considered to be reversible, otherwise irreversible. A reaction id is generated for each exchange reaction by prepending the metabolite id's with the string "Ex_".

References

Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø. and Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2, 727--738.

Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., Kang, J., Hyduke, D. R. and Palsson, B. Ø. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6, 1290--1307.

See Also

modelorg and addReact

Examples

# add exchange reactions (allowing input) for the metabolites
  # malate and oxalacetate
  data(Ec_core)
  mod <- addExchReact(Ec_core,
                      met = c("mal_L[c]", "oaa[c]"),
                      lb = c(-20, -20))
  findExchReact(mod)