Beginner's Guide

What is Julia?

"Julia is a high-level, high-performance dynamic programming language […]". You may read more about Julia here.

How do I get Julia?

You may download Julia as explained here. Please read through the Julia documentation if this is your first time trying out Julia.

How do I use Julia?

On Windows, click on the executable .exe to start Julia. You may launch Julia on Linux or macOS by in a terminal window:

julia

You should then see the prompt of Julia:

julia>

You are now in the so-called REPL. Here, you can type all Julia-commands. You can quit Julia by typing

julia> quit()

or hitting CTRL-d.

What if I need help?

If you need help, you can always type a ?at the Julia REPL. For instance, if you require assistance with the abs (absolute value) function, you may type (in the Julia REPL next to julia>):

? abs

You may also find the FAQ section of this documentation interesting, especially if you are running into issues.

How do I install a solver?

Please make sure that you have at least one of the supported solvers installed on your system.

In order to get you started, you may install the Clp solver using:

julia> Pkg.add("Clp")

This might take a while, as the Clp solver is downloaded to your system and then installed.

What if I want another solver?

As an example, and in order to get you started quickly, you may install the GLPK solver. On Windows, please follow these instructions. You must have cmake installed and gcc as described here and here.

On Linux, type:

sudo apt-get install cmake glpk-utils python-glpk libgmp-dev hdf5-tools

On macOS, you may install GLPK by using brew:

brew install glpk

In order to be able to use the GLPK solver, you must add the GLPKMathProgInterface and GLPK packages (see their respective GitHub pages here and here):

Pkg.add("GLPK")
Pkg.add("GLPKMathProgInterface")

Other supported solvers, such as CPLEX, Clp, Gurobi, or Mosek, may be installed in a similar way. Their respective interfaces are described here. If you want to use CPLEX, you must follow the installation instructions here. Most importantly, make sure that you set the LD_LIBRARY_PATH environment variable.

Now I have a solver, and I have Julia. What is next?

You are now all set to install COBRA.jl. Follow the installation instructions here. You may then also follow this tutorial to get you started.

There is a tutorial, but I cannot open it. What should I do?

If you wish to install Jupyter notebook on your own system, you may download Jupyter notebook from here.

Please make sure that you have at least Julia 0.5 as a kernel when running the Jupyter notebook. You may install the Julia kernel by launching Julia and running the following command from within the Julia REPL (as explained here):

Pkg.add("IJulia")

You have a working kernel if you see in the top right corner the name of the Julia kernel (Julia 0.5).

Please note that before adding the IJulia package, you must have followed the Jupyter installation instructions. If you are running into any issue running this tutorial on either Jupyter notebook, try it out locally by downloading first Julia as explained here.

Now, you can start the Jupyter notebook. On Linux, you may start Jupyter with:

jupyter notebook

You are all set and can run the tutorial.