2013 Complexity and Modeling Program Readings: Difference between revisions

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 {{2013 Complexity and Modeling Program}}
+==Readings and Materials==
+===General Agent-Based Modeling===
+[[Media:Axtell,_et_al_-_Aligning_Simulation_Models.pdf | Aligning Simulation Models - Axtell et al.]]
+[[Media:Epstein_-_Agent-based_Generative_Social_Science.pdf | Agent-Based Generative Social Science - Epstein‎]]
+[[Media:Epstein,_Steinbruner,_Parker_-_Modeling_Civil_Violence.pdf | Modeling Civil Violence - Epstein‎]]
+[[Media:Gajardo,_Moreira,_Goles_-_Complexity_of_Langton's_Ant.pdf | Complexity of Langton's Ant - Gajardo, Moreira, and Goles]]
+===Tasmanian Devils===
+[[Media:Polygons.PNG |Polygons.PNG]]
+===Rock, Paper, Scissors===
+[[Media:Kerr,_et_al_-_Local_dispersal_promotes_biodiversity_in_rock-paper-scissors.pdf | Rock Paper Scissors in Bacteria & Biodiversity - Kerr et al.]]‎
+[[Media:Szabo,_Szolnoki,_Izsak_-_RPS_on_Small_World_Networks.pdf | RPS on a Small World Network - Szabo, Szolnoki, Izsak]]
+[[Media:Kircher_-_Emergent_Behavior_of_Rock-Paper-Scissors_Game.pdf‎ | Emergent Behavior of Rock Paper Scissors - Kircher]]
+===Flocking===
+[[Media:Feder_-_Statistical_Physics_is_for_the_Birds.pdf | Statistical Physics is for the Birds - Feder ]]
+[[Media:Hartman,_Benes_-_Autonomous_Boids.pdf | Autonomous Boids - Hartman & Benes]]‎
+[[Media:Reynolds_-_Flocks,_Herds,_and_Schools.PDF | Flocks, Herds, and Schools - Reynolds]]‎
+===Peppered Moths: Melanism and Evolution===
+[[Media:melanism.pdf | Fine-tuning the Peppered Moth Paradigm - Grant ]]
+[[Media:Darwiniandisciple.pdf | The Peppered Moth: Decline of a Darwinian Disciple - Majerus ]]
+[[Media:Swedentalk220807.pdf | The Peppered Moth: The Proof of Darwinian Evolution - Majerus ]]
+===Chaos Theory===
+[[Media:Lorenz_-_Deterministic,_Non-periodic_Flow.PDF | Deterministic Nonperiodic Flow - Lorenz]]‎
+===Networks===
+[[Media:Dunne_-_Encyclopedia_of_Complex_Systems,_Food_Webs.pdf | Food Webs - Dunne]]
+===Ants===
+[[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 ]]
+===Modeling Complexity in Evolution===
+==== Schedule and handouts ====
+* [[Media:schedule.pdf|Schedule]]
+* [[Media:netlogo_day1_drift-mutation.pdf|Netlogo - day 1 - drift and mutation]]
+* [[Media:netlogo_day2_cooperation.pdf|Netlogo - day 2 - cooperation]]
+* [[Media:game_instructions.pdf|Instructions for online economic game]]
+==== NetLogo files ====
+* [[https://www.dropbox.com/s/tctj53o64p2u5k2/GenDriftBasic.nlogo Day 1 - drift and mutation]]
+* [[https://www.dropbox.com/s/mwyno2gpuhdcfxi/Altruism_basic.nlogo Day 2 - cooperation]]
+====Readings====
+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.
+Day 1:
+# [[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.]]
+# [[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]]
+# [[Media:Doolittle_2012_Nature.pdf|Doolittle, W. Ford. 2012. Evolutionary biology: A ratchet for protein complexity. ''Nature'' 481:270--271. doi:10.1038/nature10816]]
+Day 2:
+# [[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]]
+# [[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]]
+# [[Media:Okasha_2010_CurrBiol.pdf|Okasha, Samir. 2010. Levels of selection. ''Current Biology'' 20:R306-7. doi:10.1016/j.cub.2010.01.025]]
+===Epidemiology===
+Global Epidemic and Mobility modeler:
+[http://www.gleamviz.org/]
+Readings:
+[http://www.pnas.org/content/103/7/2015.full.pdf+html Article on the role of airline network in predicting global epidemics.]
+[http://www.cpt.univ-mrs.fr/~barrat/bmb68.pdf Maps and cartograms of disease evolution in the US via air traffic.]
+==Curriculum & Tools==
+[[Media:NetLogo_Mystery_Pattern.pdf | Netlogo Mystery Pattern]]‎
+[[Media:A1-Complex_Adaptive_Systems-W&T.doc | Walk & Turn (doc)‎]]
+[[Media:C1-Swords&Shields.doc‎ | Swords & Shields (doc)]]
+[http://projectguts.org/files/Lorenz_0.nlogo Lorenz Attractor Netlogo Program ]
+==Suggested Readings==
+[[Media:Why_Model.pdf‎ |Why Model? - Joshua M Epstein, ]]
+[http://www.santafe.edu/media/workingpapers/10-12-033.pdf Jim Crutchfield, The Dreams of Theory]
+[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]
+[http://www.amazon.com/Honeybee-Democracy-Thomas-D-Seeley/dp/0691147213  Thomas D. Seeley, Honey Bee Democracy]
+==Suggested Videos==
+[http://santafe.edu/research/videos/catalog/ Video Catalog of SFI Lectures]
+[http://itunes.apple.com/itunes-u/understanding-human-behavior/id381962164 Iain Couzin, Understanding Human Behavior]
+[http://www.youtube.com/watch?v=ZbK92bRW2lQ Hunting the Hidden Dimension, NOVA documentary on fractal geometry]
+[http://www.youtube.com/watch?v=cPjv5gIUeU8 The Secret Life of Chaos, BBC documentary on chaos theory]
+[http://www.pbs.org/wgbh/nova/nature/emergence.html Emergence, Abridged NOVA ScienceNOW documentary on emergent phenomena]
+[http://projectguts.org/files/Fileshare_Area493/videoTutorials/introCAS.mov Progect GUTS Intro to Complex Adaptive Systems]

2013 Complexity and Modeling Program Readings: Difference between revisions

From Santa Fe Institute Events Wiki

Latest revision as of 16:24, 6 August 2013

Contents

Readings and Materials

General Agent-Based Modeling

Tasmanian Devils

Rock, Paper, Scissors

Flocking

Peppered Moths: Melanism and Evolution

Chaos Theory

Networks

Ants

Modeling Complexity in Evolution

Schedule and handouts

NetLogo files

Readings

Epidemiology

Curriculum & Tools

Suggested Readings

Suggested Videos