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Agent‐based models in translational systems biology

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Abstract Effective translational methodologies for knowledge representation are needed in order to make strides against the constellation of diseases that affect the world today. These diseases are defined by their mechanistic complexity, redundancy, and nonlinearity. Translational systems biology aims to harness the power of computational simulation to streamline drug/device design, simulate clinical trials, and eventually to predict the effects of drugs on individuals. The ability of agent‐based modeling to encompass multiple scales of biological process as well as spatial considerations, coupled with an intuitive modeling paradigm, suggests that this modeling framework is well suited for translational systems biology. This review describes agent‐based modeling and gives examples of its translational applications in the context of acute inflammation and wound healing. Copyright © 2009 John Wiley & Sons, Inc. This article is categorized under: Analytical and Computational Methods > Computational Methods

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Description of the three zones of activity of the Basic Immune Simulator (BIS). (a) zone 1 is the parenchymal tissue zone. This represents a generic functional tissue (yellow circles represent parenchymal cell agents) that becomes infected with a virus (represented as the red, diffusing signal). If the average diameter of a cell to be approximated to be 0.01 mm, then zone 1 represents an area of approximately 1.0 mm2 of tissue. 1b zone 2 is the secondary lymphoid tissue zone. Secondary lymphoid tissue includes the lymph nodes and spleen. This is the site where the lymphoid cells, represented as B cell agents, T cell agents, and cytotoxic T lymphocyte agents, reside. This is also the site where agents representing antigen presenting cells (dendritic cell agents) interact with the lymphoid agents causing them to proliferate. (c) Zone 3 is the blood and lymphatic circulation, and represents a transitional space between the site of initial infection (zone 1) and the lymphoid tissue (zone 2). As the agents in the secondary lymphoid tissue proliferate (zone 2) they migrate into the lymph/blood (zone 3) and then travel back to the initial infection site (zone 1). This ABM was created using RePast software. (Reprinted with permission from Ref 22. Copyright 2007 http://www.biomedcentral.com).

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Chronic hepatitis C infection leads to hepatocellular carcinoma. Panel (a) shows a model simulation of viral levels after infection with hepatitis C. As reflected in clinical presentation measured by ALT levels, the typical course of infection shows an acute peak in viral load, followed by a low, chronic presence of the virus over a long period of time. Panel (b) shows the agents involved as inflammation progresses. Green represent healthy hepatocytes, gray are infected hepatocytes. As infected hepatocytes age and die, they become lighter in shade and turn white when dead, releasing virus (small black dots). The damage caused by infection and cell death provokes an inflammatory response mediated by macrophages (cyan circles), which secrete proinflammatory and anti‐inflammatory cytokines. This promotes growth of the initial tumor cells (black mass in the center) over the course of years. Panel (c) shows hepatocellular carcinoma after a few decades of chronic inflammation. Tumor‐associated macrophages cluster within the tumor, which develops a hypoxic core with both cancer and dead cells, and angiogenesis (red) as the mass becomes malignant. This ABM was created using SPARK software. ALT, alanine transaminase; ABM, agent‐based model; SPARK, Simple Platform for Agent‐based Representation of Knowledge.

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Simulated spheroid tumor growth using axiomatic operating principles (rules). Panel (a) demonstrates the relationship between the simulated multicellular tumor spheroids (SMS) and EMT6 spheroids (in vitro mouse mammary tumor cell cultures). An SMS is comprised of agents simulating quasi‐autonomous cell components interacting with surrounding agents and their environment using a set of axiomatic operating principles (rules). There is a clear mapping between the SMS components and the EMT6 counterparts. Following execution, the interacting components cause local and systemic behaviors. Measures of cell and system behaviors provide a set of attributes—the SMS phenotype. These attributes were calibrated to a target set of EMT6 attributes, suggesting a semiquantitative mapping between in silico and in vitro events. Panels (b) and (c) demonstrate the behavior of the SMS, with white circles = proliferating ‘cells’; light gray circles = quiescent ‘cells’; dark gray circles = ‘necrotic cells.’ The background gradient (from red to black) represent ‘nutrient’ levels relative to the maximum level in red. Panel (b) demonstrates growth in a high ‘nutrient’ environment, while panel (c) demonstrates growth in a low ‘nutrient’ environment. This ABM was created using Mason software. (Reprinted with permission from Ref 13. Copyright 2008. ABM, agent‐based model.).

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The multi‐bilayer topology of the gut–lung ABM. Cubes and spheres are cell‐level agents; these agents incorporate molecular‐level rule systems (scale‐level 1). These rule systems result in cellular behaviors (scale‐level 2). Panel (a) is the pulmonary bilayer, with aqua cubes representing pulmonary epithelial cell agents, red cubes representing pulmonary endothelial cell agents, and below are spherical inflammatory cell agents. Panel (b) is the gut bilayer, with a similar configuration, the only difference being that gut epithelial cell agents are pink. Each of these bilayers therefore represents an abstracted organ system (scale‐level 3). Circulating inflammatory cell agents move between these two bilayers. Additionally, bilayer level aggregated‐variables representing inflammatory mesenteric lymph and blood‐borne oxygen also move between the simulated gut and lung. This interconnection models the gut–lung axis, or multiorgan cross talk (scale‐level 4). This ABM was created using NetLogo software. ABM, agent‐based model. (Reprinted with permission from Ref 5. Copyright 2008 http://www.biomedcentral.com).

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