Additional MATLAB packages¶

MATLAB itself contains a set of packages which might not be a part of the core MATLAB installation, but which are often useful. These include e.g. the Statistics and Machine Learning Toolbox, Global Optimization Toolbox, and Parallel Computing Toolbox packages. These can be installed by re-running the MATLAB installer again, and selecting to install the additional packages.

IQM tools¶

IQM tools is a package developed by IntiQuan for simulating ODE models in MATLAB in a fast way, by converting the equations to C-code. Recent versions of MacOS/Xcode have problems with the latest officially released version, but we have patched this issue in a custom version of the toolbox. You can download the patched version here.

Installing IQM tools

Start with downloading IQM toolbox, and extracting the files somewhere. Then, navigate in MATLAB to your extracted IQM folder and run installIQMtoolsInitial.m (easiest is to just drag this file into the MATLAB command window). This will compile the simulation toolbox and make it usable in MATLAB. The next time you start MATLAB, you do not have to compile the toolbox again, but you will need to make it available again. To make it available again (without recompiling) run installIQMtools.m. You can now move back to the folder where you will work.

MEIGO¶

MEIGO is a toolbox for optimization, useful for e.g., estimating model parameter values.

Installing MEIGO

To install the MEIGO toolbox, download the files. Extract the files and make it usable by running install_MEIGO.m from the extracted MEIGO folder. If you restart MATLAB, you will need to run the install_MEIGO.m tools again.

Testing the packages¶

A small script to test if the toolboxes are installed correctly and available to MATLAB is available here. Currently, it checks the availability of the official MATLAB toolboxes, MEX compilation capability and compilation/simulation capabilities of the IQM tools package.

AMICI (not used in the courses on this page)¶

AMICI is a package for simulating ODE models specified in the SBML format. It is using C in the background, and is able to both simulate the model and do parameter estimation.

Installing AMICI

Download the AMICI package from here and extract the files. Then, navigate in MATLAB to the matlab folder in the the extracted AMICI folder and run installAMICI.m (easiest is to just drag this file into the MATLAB command window).