A distributed implementation of the island model for parameter fitting of dynamical systems biology models. Uses Spark (on Python) for distributed computing, pygmo2 for its various optimization algorithms, and the Tellurium environment for model simulation.

• The application business logic is contained in the sabaody directory. This includes the interface with pygmo, the migration logic, the central migration server, and the logic for calculating RMS errors for transient simulations.
• Runnable scripts are contained in the scripts directory. For example, to run the parameter fitting routine for model B2, the b2-driver.py file can be run via spark-submit as follows:

$ cd sabaody/scripts/b2
$ spark-submit --master spark://spark-master:7077 --deploy-mode client --driver-memory 1g --num-executors 4 --executor-cores 2 --files=../../../sbml/b2.xml --py-files=data.py,b2problem.py,params.py,b2setup.py b2-driver.py

• Finally, pytest tests are located in tests.