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

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

Alexey Solovyev, Maxim Mikheev, Leming Zhou, Joyeeta Dutta-Moscato, Cordelia Ziraldo, Gary An, Yoram Vodovotz, Qi Mi
Copyright: © 2010 |Volume: 2 |Issue: 3 |Pages: 13
ISSN: 1943-0744|EISSN: 1943-0752|EISBN13: 9781609609306|DOI: 10.4018/jats.2010070102
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MLA

Solovyev, Alexey, et al. "SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling." IJATS vol.2, no.3 2010: pp.18-30. http://doi.org/10.4018/jats.2010070102

APA

Solovyev, A., Mikheev, M., Zhou, L., Dutta-Moscato, J., Ziraldo, C., An, G., Vodovotz, Y., & Mi, Q. (2010). SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling. International Journal of Agent Technologies and Systems (IJATS), 2(3), 18-30. http://doi.org/10.4018/jats.2010070102

Chicago

Solovyev, Alexey, et al. "SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling," International Journal of Agent Technologies and Systems (IJATS) 2, no.3: 18-30. http://doi.org/10.4018/jats.2010070102

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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.

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