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. 2010;2(3):18-30.
doi: 10.4018/jats.2010070102.

SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling

Alexey Solovyev  1 , Maxim Mikheev, Leming Zhou, Joyeeta Dutta-Moscato, Cordelia Ziraldo, Gary An, Yoram Vodovotz, Qi Mi
Affiliations

SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling

Alexey Solovyev et al. Int J Agent Technol Syst. 2010.

Abstract

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.

Keywords: Agent-Based; Computer Simulation; Framework; Models; SPARK.

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Figures

Figure 1
Figure 1
Main components of SPARK
Figure 2
Figure 2
UML diagram showing connections between main SPARK model components
Figure 3
Figure 3
SPARK model and simulation process
Figure 4
Figure 4
SPARK user interface
Figure 5
Figure 5
Examples of SPARK models
See this image and copyright information in PMC

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