User: Docgca

 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.