Schematic of a BSim model.

BSim models consist of two main levels: 1. the individual agent (top) and 2. the shared environment (bottom). Individual agents are used to model any autonomous entity, such as a bacterium, outer membrane vesicle, etc, and contain an internal state vector which can change over time. BSim provides support for ordinary differential equations or user defined rules when specifying agent dynamics. Agents can sense various environmental factors as inputs and generate outputs within the local environment. The environment provides a shared medium in which agents can move, communicate (using chemical signaling), interact (through physical contact) with other agents or objects, and can be detailed and heterogeneous.