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. Instructions for running the scripts are here.
- Finally, pytest tests are located in tests.