User:Gary An

Current Position:

Associate Professor of Surgery

Section of General Surgery

Department of Surgery

University of Chicago Pritzker School of Medicine

Contact Information

5841 South Maryland Ave

MC5031 S-032

Chicago, IL 60637

Phone: 773-702-9742

Email: docgca@aol.com or docgca@gmail.com

Current Research

My research focuses on the utilization of agent-based modeling for multi-scale modeling of acute inflammation. Agent levels include cells and molecules, with the goal of simulating organ- and organism-level behaviors from these generative mechanisms. While the focus of my models have primarily been on the pathophysiology of sepsis and multiple organ failure, in a more general sense I am interested in using agent-based modeling as a means of dynamic knowledge representation to augment the biomedical research process. With respect to acute inflammation, the ubiquitousness of the underlying cellular and molecular mechanisms suggest the application of this methodology to such area as oncogenesis, transplant immunology/rejection, autoimmune disease, wound healing/scarring, atherosclerosis and aging. I am currently using NetLogo as my primary agent-based modeling platform, but am involved with the development of SPARK (Simple Platform for Agent-based Representation of Knowledge http://www.pitt.edu/~cirm/spark/ ) currently being done at the University of Pittsburgh. I am also interested in automated text analysis/information extraction from biomedical texts, formal knowledge representation in biomedicine and the development of methods for evolving biomedical ontologies. These goals form a "front-end" to high-level modeling tools (such as MetaABM http://www.metascapeabm.com/ ) and are intended to facilitate the ability for biomedical knowledge to be represented, communicated and evaluated via executable models. I am also involved in projects directed at developing methods to execute ABMs on massively parallel computing platforms. I believe this is a vital development necessary for true, multi-scale, biologically relevant simulation.

Complexity/Agent Based Modeling Publications

An, G and Wilensky, U. From Artificial Life to In Silico Medicine: NetLogo as a Means of Translational Knowledge Representation in Biomedical Research. In Adamatsky, A and Komosinski, M. (eds): Artificial Life in Software (Second Edition). Springer-Verlag, London, in press.

An, G: Dynamic Knowledge Representation using Agent Based Modeling: Ontology Instantiation and Verification of Conceptual Models. In Maly, I. (ed): Systems Biology: Methods in Molecular Biology Series. Humana Press, New York City, 2009.

An G. A model of TLR4 signaling and tolerance using a qualitative, particle-event-based method: Introduction of Spatially Configured Stochastic Reaction Chambers (SCSRC). Mathematical Biosciences 2009; 217:43-52.

An G. and Faeder JR. Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. Mathematical Biosciences 2009; 217:53-63.

Vodovotz Y, Constantine G, Rubin J, Csete M, Voit EO and An G. Mechanistic Simulations of Inflammation: Current State and Future Prospects. Mathematical Biosciences 2009; 217:1-10.

An G. Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation. Theoretical Biology and Medical Modelling 2008; 5:11 (May 27, 2008).

Vodovotz Y, Csete M, Bartels J, Chang S and An G. Translational Systems Biology of Inflammation. PLoS Comput Biol 4(4): e1000014. doi:10.1371/journal.pcbi.1000014

An G, Faeder J and Vodovotz Y. A Review of Translational Systems Biology as applied to Inflammation: Introduction of an Engineering Approach to the Pathophysiology of the Burn Patient. J Burn Care Res 2008; 29(2):277-285.

Folcik VA, An G and Orosz CG. The Basic Immune Simulator: an agent-based model to study the interactions between innate and adaptive immunity. Theoretical Biology and Medical Modelling 2007; 4:39, Publish ahead of print September 27, 2007.

An, G: Agent Based Modeling and Endothelial Biomedicine. In Aird, W. (ed): Endothelial Biomedicine: A Comprehensive Treatise. Cambridge University Press, 2007. Pages 1754-1759.

An G, Hunt CA, Clermont G, Neugebauer EA and Vodovotz Y. Challenges and Rewards on the Road to Translational Systems Biology in Acute Illness: Four Case Reports from Interdisciplinary Teams. Journal of Critical Care 2007; 22(2):169-175.

Vodovotz Y, Clermont G, Hunt CA, Lefering R, Bartels J, Seydel R, Hotchkiss J, Ta’asan S, Neugebauer EA and An G. Evidence-based Modeling of Critical Illness: An Initial Consensus from the Society of Complexity in Acute Illness. Journal of Critical Care 2007; 22(1):77-84.

Wakeland, W., Macovsky, L. and An, G.. A Hybrid Simulation for Studying Acute Inflammatory Response. Proceedings of the 2007 Spring Simulation Multiconference (Agent-directed Simulation Symposium). 1:39-46.

An G. Concepts for developing a collaborative in-silico model of the acute inflammatory response using agent based modeling. Journal of Critical Care 2006; 21(1): 105-110.

An G. Phenomenological issues related to measurement, mechanisms and manipulation of complex biological systems. Critical Care Medicine 2006; 34(1): 245-246. (Editorial)

An G. Introduction of an in-sIlico syntactical grammar for translating basic science research into agent based models of the acute inflammatory response. Proceedings from the 11th Congress European Shock Society 2005, H Redl editor. 161-165.

An G. Mathematical modeling in medicine: A means not an end. Critical Care Medicine 2005; 33(1): 253-254. (Editorial)

Vodovotz Y, Clermont G, Chow C, An G. Mathematical models of the acute inflammatory response. Current Opinions in Critical Care 2004; 10:383-390.

An G. In-silico experiments of existing and hypothetical cytokine-directed clinical trials using agent based modeling. Critical Care Medicine 2004; 32(10): 2050-2060..

An G. Complexity theory and surgery: Introducing and integrating a new analytical paradigm. New Surgery 2001; 1(3): 175-179.

An G. Agent-based computer simulation and SIRS: Building a bridge between basic science and clinical trials. Shock 2001; 16(4): 266-273.

An G, Lee I. Agent-Based Computer simulation (ABCS) and the inflammatory response: Building a tool to study Systemic Inflammatory Response Syndrome (SIRS). Simulation and Gaming 2001; 32(3): 344-361.

An G, Lee I. Complexity, Emergence and Pathophysiology: Using Agent Based Computer Simulation to characterize the Non-Adaptive Inflammatory Response. InterJournal Complex Systems: http://www.interjournal.org. Manuscript # [344]. May, 2000.

Links

Link to Society of Complexity in Acute Illness (SCAI). This is an organization of physicians and biomedical researchers committed to promoting the use of mathematical modeling and computational methods to analyze the pathophysiology of acute illnesses with a focus on inflammation. http://www.scai-med.org

Link to Modeling Glossary developed and maintained by the Biosystems Research Group at the University of California, San Francisco under the leadership of C. Anthony Hunt. This Glossary can be used as a reference point by those interested in biomedical modeling as a means of fostering communication between modelers and domain specialists. http://biosystems.ucsf.edu/Researc/dictionary.html