To run the desired example, launch gradle -Psim=THESIMULATIONFILE, where THESIMULATIONFILE must be the name of a valid Alchemist YAML file in src/main/yaml. For instance, to launch the first example, use this command:
gradlew -Psim=00-minimal
If an effects file with the same name of the YAML file is present in the effects folder, it will be loaded automatically.
Some tutorial simulations are already in src/main/yaml, you can add your own to make tests and learn Alchemist Biochemistry.