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| [[Image: SFIcamp20143.jpg]] | | [[Image: SFIcamp20143.jpg]] |
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| ==Readings and Materials==
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| ===General Agent-Based Modeling===
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| [[Media:Axtell,_et_al_-_Aligning_Simulation_Models.pdf | Aligning Simulation Models - Axtell et al.]]
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| [[Media:Epstein_-_Agent-based_Generative_Social_Science.pdf | Agent-Based Generative Social Science - Epstein]]
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| [[Media:Epstein,_Steinbruner,_Parker_-_Modeling_Civil_Violence.pdf | Modeling Civil Violence - Epstein]]
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| [[Media:Gajardo,_Moreira,_Goles_-_Complexity_of_Langton's_Ant.pdf | Complexity of Langton's Ant - Gajardo, Moreira, and Goles]]
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| ===Tasmanian Devils===
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| [[Media:Polygons.PNG |Polygons.PNG]]
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| ===Rock, Paper, Scissors===
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| [[Media:Kerr,_et_al_-_Local_dispersal_promotes_biodiversity_in_rock-paper-scissors.pdf | Rock Paper Scissors in Bacteria & Biodiversity - Kerr et al.]]
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| [[Media:Szabo,_Szolnoki,_Izsak_-_RPS_on_Small_World_Networks.pdf | RPS on a Small World Network - Szabo, Szolnoki, Izsak]]
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| [[Media:Kircher_-_Emergent_Behavior_of_Rock-Paper-Scissors_Game.pdf | Emergent Behavior of Rock Paper Scissors - Kircher]]
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| ===Flocking===
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| [[Media:Feder_-_Statistical_Physics_is_for_the_Birds.pdf | Statistical Physics is for the Birds - Feder ]]
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| [[Media:Hartman,_Benes_-_Autonomous_Boids.pdf | Autonomous Boids - Hartman & Benes]]
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| [[Media:Reynolds_-_Flocks,_Herds,_and_Schools.PDF | Flocks, Herds, and Schools - Reynolds]]
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| ===Peppered Moths: Melanism and Evolution===
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| [[Media:melanism.pdf | Fine-tuning the Peppered Moth Paradigm - Grant ]]
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| [[Media:Darwiniandisciple.pdf | The Peppered Moth: Decline of a Darwinian Disciple - Majerus ]]
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| [[Media:Swedentalk220807.pdf | The Peppered Moth: The Proof of Darwinian Evolution - Majerus ]]
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| ===Chaos Theory===
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| [[Media:Lorenz_-_Deterministic,_Non-periodic_Flow.PDF | Deterministic Nonperiodic Flow - Lorenz]]
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| ===Networks===
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| [[Media:Dunne_-_Encyclopedia_of_Complex_Systems,_Food_Webs.pdf | Food Webs - Dunne]]
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| ===Ants===
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| [[Media:Dorigo,_Maniezzo,_Colorni_-_The_Ant_System_-_Optimization_by_a_colony_of_cooperating_agents.pdf | The Ant System: Optimization by a Colony of Cooperating Agents - Dorigo, Maniezzo, Colorni ]]
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| ===Modeling Complexity in Evolution===
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| ==== Schedule and handouts ====
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| * [[Media:schedule.pdf|Schedule]]
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| * [[Media:netlogo_day1_drift-mutation.pdf|Netlogo - day 1 - drift and mutation]]
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| * [[Media:netlogo_day2_cooperation.pdf|Netlogo - day 2 - cooperation]]
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| * [[Media:game_instructions.pdf|Instructions for online economic game]]
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| ==== NetLogo files ====
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| * [[https://www.dropbox.com/s/tctj53o64p2u5k2/GenDriftBasic.nlogo Day 1 - drift and mutation]]
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| * [[https://www.dropbox.com/s/mwyno2gpuhdcfxi/Altruism_basic.nlogo Day 2 - cooperation]]
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| ====Readings====
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| In order to help you prioritize, the first reading for each day is the most important, while the second is important and the third is less important.
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| Day 1:
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| # [[Media:McShea.Brandon_2010_BiologysFirstLaw_Chapter1.pdf|McShea, Daniel W and Brandon, Robert N. 2010. ''Biology's first law: the tendency for diversity and complexity to increase in evolutionary systems''. University of Chicago Press, Chicago. Chapter 1.]]
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| # [[Media:Zimmer_2013_SciAm.pdf|Zimmer, Carl. 2013. The Surprising Origins of Life's Complexity. ''Scientific American'' 309:84--89. doi:10.1038/scientificamerican0813-84]]
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| # [[Media:Doolittle_2012_Nature.pdf|Doolittle, W. Ford. 2012. Evolutionary biology: A ratchet for protein complexity. ''Nature'' 481:270--271. doi:10.1038/nature10816]]
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| Day 2:
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| # [[Media:Szathmary.MaynardSmith_1995_Nature.pdf|Szathmáry, Eörs and Maynard Smith, John. 1995. The major evolutionary transitions. ''Nature'' 374:227--232. doi:10.1038/374227a0]]
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| # [[Media:Godfrey-Smith_2006_BiolTheory.pdf|Godfrey-Smith, Peter. 2006. Local Interaction, Multilevel Selection, and Evolutionary Transitions. ''Biological Theory'' 1:372--380. doi:10.1162/biot.2006.1.4.372]]
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| # [[Media:Okasha_2010_CurrBiol.pdf|Okasha, Samir. 2010. Levels of selection. ''Current Biology'' 20:R306-7. doi:10.1016/j.cub.2010.01.025]]
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| ===Epidemiology===
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| Global Epidemic and Mobility modeler:
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| [http://www.gleamviz.org/]
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| Readings:
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| [http://www.pnas.org/content/103/7/2015.full.pdf+html Article on the role of airline network in predicting global epidemics.]
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| [http://www.cpt.univ-mrs.fr/~barrat/bmb68.pdf Maps and cartograms of disease evolution in the US via air traffic.]
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| ==Curriculum & Tools==
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| [[Media:NetLogo_Mystery_Pattern.pdf | Netlogo Mystery Pattern]]
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| [[Media:A1-Complex_Adaptive_Systems-W&T.doc | Walk & Turn (doc)]]
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| [[Media:C1-Swords&Shields.doc | Swords & Shields (doc)]]
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| [http://projectguts.org/files/Lorenz_0.nlogo Lorenz Attractor Netlogo Program ]
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| ==Suggested Readings==
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| [[Media:Why_Model.pdf |Why Model? - Joshua M Epstein, ]]
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| [http://www.santafe.edu/media/workingpapers/10-12-033.pdf Jim Crutchfield, The Dreams of Theory]
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| [http://www.amazon.com/Complexity-Guided-Tour-Melanie-Mitchell/dp/0195124413/ref=sr_1_1?ie=UTF8&qid=1309386862&sr=8-1 Melanie Mitchell, Complexity: A Guided Tour]
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| [http://www.amazon.com/Honeybee-Democracy-Thomas-D-Seeley/dp/0691147213 Thomas D. Seeley, Honey Bee Democracy]
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| ==Suggested Videos==
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| [http://santafe.edu/research/videos/catalog/ Video Catalog of SFI Lectures]
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| [http://itunes.apple.com/itunes-u/understanding-human-behavior/id381962164 Iain Couzin, Understanding Human Behavior]
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| [http://www.youtube.com/watch?v=ZbK92bRW2lQ Hunting the Hidden Dimension, NOVA documentary on fractal geometry]
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| [http://www.youtube.com/watch?v=cPjv5gIUeU8 The Secret Life of Chaos, BBC documentary on chaos theory]
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| [http://www.pbs.org/wgbh/nova/nature/emergence.html Emergence, Abridged NOVA ScienceNOW documentary on emergent phenomena]
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| [http://projectguts.org/files/Fileshare_Area493/videoTutorials/introCAS.mov Progect GUTS Intro to Complex Adaptive Systems]
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