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Agent-Based Modeling Approaches to Multi-Scale Systems Biology: An Example Agent-Based Model of Acute Pulmonary Inflammation

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Systems Biology

Abstract

Implicit in systems biology is the concept that the whole is greater than the sum of its parts. Agent-based modeling, an object-oriented, discrete event, population-based computational modeling method, is well suited to meeting this goal. By viewing systems as aggregates of populations of interacting components, agent-based models (ABMs) map well to biological conceptual models and present an intuitive means by which biomedical researchers can represent their knowledge in a dynamic computational form. ABMs are particularly suited for representing the behaviour of populations of cells (i.e. “cell-as-agents”), but ABMs have also been used to model molecular interactions, particularly when spatial and structural properties are involved. Presented herein are a series of ABMs of biomedical systems that cross multiple scales of biological organization, as well as a detailed description of an example ABM of acute pulmonary inflammation. Because of these characteristics agent-based modeling is a useful addition to the suite of equation-based mathematical modeling methods found in systems biology, and can serve as an integrating framework for dynamic knowledge representation of biological systems.

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Abbreviations

ABM:

Agent-Based Modeling

ABMF:

Agent-Based Modeling Format

AI:

Artificial Intelligence

ALI:

Acute Lung Injury

APIABM:

Acute Pulmonary Injury Agent-Based Model

ARDS:

Acute Respiratory Distress Syndrome

CMA:

Computational Modeling Assistant

DAMP:

Damage-Associated Molecular Products

EINISI:

Enteric Immunity Simulator

I-κB:

I-kappa-B

NCBO:

National Center for Biomedical Ontology

NEC:

Necrotizing enterocolitis

NF-κB:

Nuclear Factor kappa-B

ODD:

Overview, Design and Detail Protocol

ODE:

Ordinary differential equation

PMN:

Polymorphonuclear neutrophils

TGF-β1:

Transforming growth factor-β1

TNF-α:

Tumor necrosis factor-α

VILI:

Ventilator Induced Lung Injury

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Authors and Affiliations

  1. Department of Surgery, University of Chicago, Chicago, USA

    Gary An & Scott Christley

  2. Department of Surgery, Northwestern University, Chicago, USA

    Michael Wandling

Authors
  1. Gary An
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  2. Michael Wandling
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  3. Scott Christley
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Correspondence to Gary An .

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Editors and Affiliations

  1. Chemical and Biological Engineering, Vanderbilt University, Nashville, TN, USA

    Aleš Prokop

  2. Research Group on Process Network Engineering, Kaposvár University, Kaposvár, Hungary

    Béla Csukás

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An, G., Wandling, M., Christley, S. (2013). Agent-Based Modeling Approaches to Multi-Scale Systems Biology: An Example Agent-Based Model of Acute Pulmonary Inflammation. In: Prokop, A., Csukás, B. (eds) Systems Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6803-1_15

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