title: SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling.
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.
authors.affiliation: University of Pittsburgh, USA.
authors.forename: Alexey
authors.initials: A
authors.lastname: Solovyev
authors.forename: Maxim
authors.initials: M
authors.lastname: Mikheev
authors.forename: Leming
authors.initials: L
authors.lastname: Zhou
authors.forename: Joyeeta
authors.initials: J
authors.lastname: Dutta-Moscato
authors.forename: Cordelia
authors.initials: C
authors.lastname: Ziraldo
authors.forename: Gary
authors.initials: G
authors.lastname: An
authors.forename: Yoram
authors.initials: Y
authors.lastname: Vodovotz
authors.forename: Qi
authors.initials: Q
authors.lastname: Mi
keywords: Agent-Based; Computer Simulation; Framework; Models; SPARK