Editing Agent-based model (section)

===In biology===
{{main|Agent-based model in biology}}

Agent-based modeling has been used extensively in biology, including the analysis of the spread of [[epidemics]],<ref>{{cite arXiv |eprint=nlin/0403035 |last1=Situngkir |first1=Hokky |title=Epidemiology Through Cellular Automata: Case of Study Avian Influenza in Indonesia |year=2004}}</ref> and the threat of [[biowarfare]], [[Agent-based model in biology|biological applications]] including [[population dynamics]],<ref>{{cite journal |last=Caplat |first=Paul |author2=Anand, Madhur |author3=Bauch, Chris |title=Symmetric competition causes population oscillations in an individual-based model of forest dynamics |journal=Ecological Modelling |date=March 10, 2008 |volume=211 |issue=3–4 |pages=491–500 |doi=10.1016/j.ecolmodel.2007.10.002|bibcode=2008EcMod.211..491C }}</ref> stochastic gene expression,<ref>{{Cite journal|last=Thomas|first=Philipp|date=December 2019|title=Intrinsic and extrinsic noise of gene expression in lineage trees|journal=Scientific Reports|volume=9|issue=1|pages=474|doi=10.1038/s41598-018-35927-x|issn=2045-2322|pmc=6345792|pmid=30679440|bibcode=2019NatSR...9..474T}}</ref> plant-animal interactions,<ref>Fedriani JM, T Wiegand, D Ayllón, F Palomares, A Suárez-Esteban and V. Grimm.  2018. Assisting seed dispersers to restore old-fields: an individual-based model of the interactions among badgers, foxes, and Iberian pear trees. Journal of Applied Ecology 55: 600–611.</ref>  vegetation ecology,<ref name="Ch'ng, E. (2009)">Ch'ng, E. (2009) An Artificial Life-Based Vegetation Modelling Approach for Biodiversity Research, in Nature-Inspired informatics for Intelligent Applications and Knowledge Discovery: Implications in Business, Science and Engineering, R. Chiong, Editor. 2009, IGI Global: Hershey, PA. http://complexity.io/Publications/NII-alifeVeg-eCHNG.pdf {{Webarchive|url=https://web.archive.org/web/20131113173223/http://complexity.io/Publications/NII-alifeVeg-eCHNG.pdf |date=November 13, 2013 }}</ref> migratory ecology,<ref>{{cite report|first1=F.G.|last1=Weller|first2=E.B.|last2=Webb|first3=W.S.|last3=Beatty|first4=S.|last4=Fogenburg|first5=D.|last5=Kesler|first6=R.H.|last6=Blenk|first7=J.M.|last7=Eadie|first8=K.|last8=Ringelman |first9=M. L.|last9=Miller|year= 2022|title=Agent-based modeling of movements and habitat selection by mid-continent mallards|publisher=U.S. Department of Interior, Fish and Wildlife Service|series=Cooperator Science Series|id=FWS/CSS-143-2022|location=Washington, D. C|doi=10.3996/css47216360}}</ref> landscape diversity,<ref>{{Cite journal |last1=Wirth |first1=E. |last2=Szabó |first2=Gy. |last3=Czinkóczky |first3=A. |date=2016-06-07 |journal=ISPRS Annals of the Photogrammetry, Remote Sensing and Spatial Information Sciences |volume=III-8 |pages=145–151 |doi=10.5194/isprs-annals-iii-8-145-2016 |bibcode=2016ISPAnIII8..145W|title=Measure of Landscape Heterogeneity by Agent-Based Methodology |doi-access=free }}</ref> [[sociobiology]],<ref name=Lima2009>{{cite journal
 |first1=Francisco W.S. |last1=Lima
 |first2=Tarik |last2=Hadzibeganovic |first3=Dietrich |last3=Stauffer.
 |year=2009
 |title=Evolution of ethnocentrism on undirected and directed Barabási-Albert networks
 |journal=Physica A
 |volume=388
 |pages=4999–5004
 |doi=10.1016/j.physa.2009.08.029
 |issue=24
|arxiv=0905.2672|bibcode=2009PhyA..388.4999L|s2cid=18233740
 }}</ref> the growth and decline of ancient civilizations, evolution of ethnocentric behavior,<ref>{{cite journal |last1=Lima |first1=Francisco W. S. |last2=Hadzibeganovic |first2=Tarik |last3=Stauffer |first3=Dietrich |year=2009 |title=Evolution of ethnocentrism on undirected and directed Barabási–Albert networks |journal=Physica A |volume=388 |issue=24 |pages=4999–5004 |doi=10.1016/j.physa.2009.08.029 |bibcode=2009PhyA..388.4999L |arxiv=0905.2672 |s2cid=18233740 }}</ref> forced displacement/migration,<ref>{{cite book |title=The Chaos of Forced Migration: A Modeling Means to an Humanitarian End |first=Scott |last=Edwards |date=June 9, 2009 |publisher=[[VDM Verlag]] |pages=168 |isbn=978-3-639-16516-6}}</ref> language choice dynamics,<ref>{{cite journal |last1=Hadzibeganovic |first1=Tarik |last2=Stauffer |first2=Dietrich |last3=Schulze |first3=Christian |year=2009 |title=Agent-based computer simulations of language choice dynamics |journal=Annals of the New York Academy of Sciences |volume=1167 |issue=1|pages=221–229 |doi=10.1111/j.1749-6632.2009.04507.x |pmid=19580569 |bibcode=2009NYASA1167..221H |s2cid=32790067 }}</ref> [[Cognitive model#Dynamical systems|cognitive modeling]], and biomedical applications including modeling 3D breast tissue formation/morphogenesis,<ref>{{cite journal |last1=Tang |first1=Jonathan|author2-link=Heiko Enderling |last2=Enderling |first2=Heiko |last3=Becker-Weimann |first3=Sabine |last4=Pham |first4=Christopher |last5=Polyzos |first5=Aris |last6=Chen |first6=Charlie |last7=Costes |first7=Sylvain |year=2011 |title=Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling |journal=Integrative Biology |volume=3 |issue=4 |pages=408–21 |doi=10.1039/c0ib00092b |pmid=21373705 |pmc=4009383 }}</ref> the effects of ionizing radiation on mammary stem cell subpopulation dynamics,<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Fernando-Garcia |first2=Ignacio |last3=Vijayakumar |first3=Sangeetha |last4=Martinez-Ruis |first4=Haydeliz |last5=Illa-Bochaca |first5=Irineu |last6=Nguyen |first6=David |last7=Mao |first7=Jian-Hua |last8=Costes |first8=Sylvain |last9=Barcellos-Hoff |first9=Mary Helen |year=2014 |title=Irradiation of juvenile, but not adult, mammary gland increases stem cell self-renewal and estrogen receptor negative tumors |journal=Stem Cells |volume=32 |issue=3 |pages=649–61 |doi=10.1002/stem.1533 |pmid=24038768   |s2cid=32979016 |doi-access=free }}</ref> inflammation,<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Ley |first2=Klaus |last3=Hunt |first3=C. Anthony |year=2007 |title=Dynamics of in silico leukocyte rolling, activation, and adhesion |journal=BMC Systems Biology |volume=1 |issue=14 |pages=14 |doi=10.1186/1752-0509-1-14 |pmid=17408504 |pmc=1839892 |doi-access=free }}</ref>
<ref>{{cite journal |last1=Tang |first1=Jonathan |last2=Hunt |first2=C. Anthony |year=2010 |title=Identifying the rules of engagement enabling leukocyte rolling, activation, and adhesion |journal=PLOS Computational Biology |volume=6 |issue=2 |pages=e1000681 |doi=10.1371/journal.pcbi.1000681 |pmid=20174606 |pmc=2824748 |bibcode=2010PLSCB...6E0681T |doi-access=free }}</ref> 
and the human [[immune system]],<ref>{{cite book |last1=Castiglione |first1=Filippo |first2=Franco |last2=Celada |url=http://www.crcpress.com/product/isbn/9781466597488 |title=Immune System Modeling and Simulation |publisher=CRC Press, Boca Raton |year=2015 |pages=274 |isbn=978-1-4665-9748-8 |access-date=December 17, 2017 |archive-date=February 4, 2023 |archive-url=https://web.archive.org/web/20230204160700/https://www.routledge.com/Immune-System-Modelling-and-Simulation/Castiglione-Celada/p/book/9781466597488 |url-status=live }}</ref> and the evolution of foraging behaviors.<ref>{{cite journal |last1=Liang |first1=Tong |last2=Brinkman |first2=Braden A. W. |title=Evolution of innate behavioral strategies through competitive population dynamics |journal=PLOS Computational Biology |date=14 March 2022 |volume=18 |issue=3 |pages=e1009934 |doi=10.1371/journal.pcbi.1009934 |doi-access=free |pmid=35286315 |bibcode=2022PLSCB..18E9934L |language=en |issn=1553-7358|pmc=8947601 }}</ref> Agent-based models have also been used for developing decision support systems such as for breast cancer.<ref>{{Cite book |doi=10.1109/ICICT.2009.5267202 |chapter-url=http://www.cs.stir.ac.uk/~man/papers/ICICT_Cameraready_June20_09.pdf |url-status=dead |archive-url=https://web.archive.org/web/20110614051810/http://www.cs.stir.ac.uk/~man/papers/ICICT_Cameraready_June20_09.pdf |archive-date=June 14, 2011 |df=mdy-all |chapter=A new hybrid agent-based modeling & simulation decision support system for breast cancer data analysis |title=2009 International Conference on Information and Communication Technologies |pages=134–139 |year=2009 |last1=Siddiqa |first1=Amnah |last2=Niazi |first2=Muaz |last3=Mustafa |first3=Farah |last4=Bokhari |first4=Habib |last5=Hussain |first5=Amir |last6=Akram |first6=Noreen |last7=Shaheen |first7=Shabnum |last8=Ahmed |first8=Fouzia |last9=Iqbal |first9=Sarah |isbn=978-1-4244-4608-7 |s2cid=14433449 }} (Breast Cancer DSS)</ref> Agent-based models are increasingly being used to model pharmacological systems in early stage and pre-clinical research to aid in drug development and gain insights into biological systems that would not be possible ''a priori''.<ref name=CPT>{{cite journal |last1=Butler |first1=James |last2=Cosgrove |first2=Jason |last3=Alden |first3=Kieran |last4=Read |first4=Mark |last5=Kumar |first5=Vipin |last6=Cucurull-Sanchez |first6=Lourdes |last7=Timmis |first7=Jon |last8=Coles |first8=Mark |title=Agent-Based Modeling in Systems Pharmacology |journal=CPT: Pharmacometrics & Systems Pharmacology |date=2015 |volume=4 |issue=11 |pages=615–629 |doi=10.1002/psp4.12018 |pmid = 26783498|pmc=4716580 }}</ref> Military applications have also been evaluated.<ref>{{cite book |title=Engineering Principles of Combat Modeling and Distributed Simulation |first1=Gnana |last1=Barathy |first2=Levent |last2=Yilmaz |first3=Andreas |last3=Tolk |location=Hoboken, NJ |publisher=[[John Wiley & Sons|Wiley]] |pages=669–714 |date=March 2012 |doi=10.1002/9781118180310.ch27 |chapter=Agent Directed Simulation for Combat Modeling and Distributed Simulation |isbn=9781118180310}}</ref> Moreover, agent-based models have been recently employed to study molecular-level biological systems.<ref>{{Cite journal |last1=Azimi |first1=Mohammad |last2=Jamali |first2=Yousef |last3=Mofrad |first3=Mohammad R. K. |title=Accounting for Diffusion in Agent Based Models of Reaction-Diffusion Systems with Application to Cytoskeletal Diffusion |journal=PLOS ONE |volume=6 |issue=9 |pages=e25306 |doi=10.1371/journal.pone.0025306 |pmc=3179499 |pmid=21966493 |year=2011 |bibcode=2011PLoSO...625306A|doi-access=free }}</ref><ref>{{Cite journal |last1=Azimi |first1=Mohammad |last2=Mofrad |first2=Mohammad R. K. |title=Higher Nucleoporin-Importinβ Affinity at the Nuclear Basket Increases Nucleocytoplasmic Import |journal=PLOS ONE |volume=8 |issue=11 |pages=e81741 |doi=10.1371/journal.pone.0081741 |pmc=3840022 |pmid=24282617 |year=2013 |bibcode=2013PLoSO...881741A|doi-access=free }}</ref><ref>{{Cite journal |last1=Azimi |first1=Mohammad |last2=Bulat |first2=Evgeny |last3=Weis |first3=Karsten |last4=Mofrad |first4=Mohammad R. K. |date=2014-11-05 |title=An agent-based model for mRNA export through the nuclear pore complex |journal=Molecular Biology of the Cell |volume=25 |issue=22 |pages=3643–3653 |doi=10.1091/mbc.E14-06-1065 |pmc=4230623 |pmid=25253717}}</ref> Agent-based models have also been written to describe ecological processes at work in ancient systems, such as those in dinosaur environments and more recent ancient systems as well.<ref>{{Cite journal |last1=Pahl |first1=Cameron C. |last2=Ruedas |first2=Luis |title=Carnosaurs as Apex Scavengers: Agent-based simulations reveal possible vulture analogues in late Jurassic Dinosaurs |journal=Ecological Modelling |volume=458 |doi=10.1016/j.ecolmodel.2021.109706|year=2021|page=109706 |bibcode=2021EcMod.45809706P }}</ref><ref>{{Cite journal |last1=Volmer |display-authors=etal |date=2017 |title=Did Panthera pardus (Linnaeus, 1758) become extinct in Sumatra because of competition for prey? Modeling interspecific competition within the Late Pleistocene carnivore guild of the Padang Highlands, Sumatra |journal=Palaeogeography, Palaeoclimatology, Palaeoecology |volume=487 |pages=175–186 |doi=10.1016/j.palaeo.2017.08.032|bibcode=2017PPP...487..175V }}</ref><ref>{{Cite journal |last1=Hagen |first1=Oskar |last2=Flück |first2=Benjamin |last3=Fopp|first3=Fabian |last4=Cabral |first4=Juliano C. |last5=Hartig |first5=Florian |last6=Pontarp |first6=Mikael |last7=Rangel |first7=Thiago F. |last8=Pellissier |first8=Loïc |title=gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity |journal=PLOS Biology |volume=19|doi=10.1371/journal.pbio.3001340|year=2021|issue=7 |page=e3001340 |pmid=34252071 |pmc=8384074 |s2cid=235807562 |doi-access=free }}</ref>