This fork of the iDynoMiCS was created for comparing biofilm simulations containing planktonic agents to in-vitro biofilm experiments.
The compiled code is available in the /bin directory. With java installed on a MacOS or Linux system, the easiest way to run an example simulation is to cd into this directory and run the following for an example simulation:
python scripts_to_start_idynomics/RunIdyno.py protocol/examples/planktonic_ex.xml
For more information, see the original iDynoMiCS tutorial in the tutorial directory.