This tutorial serves as a quick start guide as well as an interactive reference for more advanced users. Download the live notebook from here.
If you do not already have the COBRA.jl package installed, you must first first follow the installation instructions here.
Please note that should you run this tutorial on an already configured system. Otherwise, the following lines will throw an error message.
Before running any function of COBRA.jl, it is necessary to include the COBRA.jl module:
In [ ]:
using COBRA
You can test your system by running:
In [ ]:
COBRA.checkSysConfig()
Should you not have any prior experience with Julia and/or Linux, please follow carefully the Beginner's Guide. If you however feel that you are set to proceed with this tutorial, please consider the Beginner's Guide as a go-to reference in case you are running into any issues.
If you see unusual behavior, you may consider reading the FAQ section.
Do you feel lost or you don’t know the meaning of certain input parameters? Try typing a question mark at the Julia REPL followed by a keyword. For instance:
julia> ? distributedFBA
Make sure that you have a working installation of MathProgBase.jl and at least one of the supported solvers. You may find further information here.
If you want to install other solvers such as CPLEX, CLP, Gurobi, or Mosek, you can find more information here.
You may, at any time, check the integrity of the COBRA.jl package by running:
julia> Pkg.test("COBRA")
The code has been benchmarked against the fastFVA implementation [3]. The modules and solvers are correctly installed when all tests pass without errors (warnings may appear).