Before revision:  In this manual , we describe how to use the software together with COMSOL Multiphysics 3.4 and Matlab to set up simulations. We provide a detailed account of the code structure and of the available interfaces. This makes modifications and extensions of the code possible. We also give two detailed examples, in which we describe the process of simulating and visualizing two models from the systems biology literature in a step-by-step manner .
After revision:  This manual describes version 1.1 of the software .