cobrarCPLEX

An extension of the R-package cobrar, which makes IBM’s ILOG CPLEX solver accessible.

Requirements

• Installed R-package cobrar
• Working CPLEX Installation version 20.1.0 or higher

Installation

You can install the development version of cobrarCPLEX like so:

remotes::install_github("Waschina/cobrarCPLEX", configure.args="--with-cplex-dir=/path/to/cplex")

Note: Please replace /path/to/cplex with the path to your cplex installation.

E.g., in unix systems, cplex is by default installed to something like /opt/ibm/ILOG/CPLEX_Studio2211/cplex. Thus the command to install cobrarCPLEX would be:

remotes::install_github("Waschina/cobrarCPLEX", configure.args="--with-cplex-dir=/opt/ibm/ILOG/CPLEX_Studio2211/cplex")

Example

This is a basic example which shows how to use cobrarCPLEX and compares the computation time for flux balance analysis:

library(cobrarCPLEX)
#> Loading required package: cobrar
#> Loading required package: Matrix
#> cobrar uses...
#>  - libSBML (v. 5.18.0)
#>  - glpk (v. 4.65)
#> Using cplex version 22010100

# Download the E. coli model "iML1515" from http://bigg.ucsd.edu/
modfile <- tempfile(fileext = ".xml.gz")
download.file("http://bigg.ucsd.edu/static/models/iML1515.xml.gz", modfile)
mod <- readSBMLmod(modfile)

# FBA with GLPK
COBRAR_SETTINGS("SOLVER","glpk")
print(system.time(fba(mod)))
#>    user  system elapsed 
#>   0.216   0.000   0.216

# FBA with CPLEX
COBRAR_SETTINGS("SOLVER","cplex")
system.time(fba(mod))
#>    user  system elapsed 
#>    0.04    0.00    0.04