SPARK: a framework for multi-scale agent-based biomedical modeling

Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK Simple Platform for Agent-based Representation of Knowledge, a framework for agent-based modeling specifically designed for systems-level biomedical model development. SPARK is a stand-alone application written in Java. It provides a user-friendly interface, and a simple programming language for developing Agent-Based Models ABMs. SPARK has the following features specialized for modeling biomedical systems: 1 continuous space that can simulate real physical space; 2 flexible agent size and shape that can represent the relative proportions of various cell types; 3 multiple spaces that can concurrently simulate and visualize multiple scales in biomedical models; 4 a convenient graphical user interface. Existing ABMs of diabetic foot ulcers and acute inflammation were implemented in SPARK. Models of identical complexity were run in both NetLogo and SPARK; the SPARK-based models ran two to three times faster.