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Table 1 Summary of the agents, signals and behaviors in the Basic Immune Simulator.

From: The Basic Immune Simulator: An agent-based model to study the interactions between innate and adaptive immunity

AGENT TYPES AND ZONES IMMUNE CELLS REPRESENTED AND FUNCTIONAL DESCRIPTION SIGNALS CYTOKINES, CHEMOKINES [28] AND MOLECULES REPRESENTED BY EACH SIGNAL
Parenchymal Cell Agent (PC) Zone 1 Functional tissue cells (Parenchymal-kine 1) PK1 Stress factors such as Heat Shock Proteins [66], Uric Acid [67], and Chemerin [68], chemokines such as CX3CL1, CCL3, CCL5, CCL6
   Virus Virus particles
   Apoptotic bodies Apoptotic bodies or dead cells associated with programmed cell death
   Necrosis factors Cell fragments associated with death by necrosis
Dendritic Cell Agent (DC1, DC2) Zones 1, 2 Tissue surveillance, antigen presentation, INNATE immunity (Mono-kine 1) MK1 IL-12, IL-8 (CXCL8) [69], CCL3, CCL4, CCL5, CXCL9, CXCL10, CXCL11
   (Mono-kine 2) MK2 IL-10, CCL1, CCL17, CCL22, CCL11, CCL24, CCL26
Macrophage Agent (MΦ1, MΦ2)Zone 1 Scavenging of dead cell debris, antigen presentation, INNATE immunity MK1 IL-12, IL-8 (CXCL8), CCL3, CCL4, CCL5, CXCL9, CXCL10, CXCL11
   MK2 IL-10, CCL1, CCL17, CCL22, CCL11, CCL24, CCL26
T Cell Agent (T, T1, T2) Zones 2,3,1 T HELPER lymphocytes, cell-mediated, ADAPTIVE immunity (Cytokine 1) CK1 IFN-γ, IL-2, TNF-β
   (Cytokine 2) CK2 TGF-β, IL-4, IL-5, IL-6, IL-10, IL-13
Cytotoxic T Lymphocyte Agent (CTL) Zones 2,3,1 T CYTOTOXIC lymphocytes, cell-mediated, ADAPTIVE immunity CK1 IFN-γ
Natural Killer Cell Agent (NK) Zone 1 Natural Killer Cells, cell-mediated immunity, kills stressed cells, INNATE immunity CK1 IFN-γ
B Cell Agent (B, B1, B2) Zones 2,3,1 B Lymphocytes, ADAPTIVE, humoral immunity, makes antibodies (Antibody 1) Ab1 Cytotoxic and neutralizing antibody
   (Antibody 2) Ab2 Targeting and neutralizing antibody
   Complement Bound antibody catalyzes complement product formation, C3a, C5a [70]
Granulocyte Agent (Gran) Zones 3,1 Neutrophils, Eosinophils and Basophils, INNATE immunity, releases enzymes and toxins by degranulation and produces reactive oxygen species (Degranulation product 1) G1 Degranulation products, reactive oxygen products
Portal Agent Zones 1,2,3 Blood vessels, lymphatic ducts. The only agent representing a structure rather than a cell type.   
  1. All of the programmed entities that exist in the simulation are listed in the "AGENT TYPES AND ZONES" and "SIGNALS" columns. The words "cell" or "lymphocyte" are meant to refer to the actual living structure. The word "agent" refers to the representation or programmed object that exists in the simulation.