2014 Complexity and Modeling Program Readings - Revision history

Juniperlovato at 14:53, 15 July 2014

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	===Resources===		===Resources===

	==[http://fractalfoundation.org/ Fractal Foundation]==		'''[http://fractalfoundation.org/ Fractal Foundation]''' <br>
	==[http://santafe.edu/ Santa Fe Institute Website]==		'''[http://santafe.edu/ Santa Fe Institute Website]'''<br>
	==[http://www.complexityexplorer.org/online-courses/11 Introduction to Complexity Online Videos]==		'''[http://www.complexityexplorer.org/online-courses/11 Introduction to Complexity Online Videos]'''<br>
	==[http://www.complexityexplorer.org/explore/glossary Complexity Explorer Terms Glossary]==		'''[http://www.complexityexplorer.org/explore/glossary Complexity Explorer Terms Glossary]'''<br>
	==[http://www.complexityexplorer.org/online-courses Santa Fe Institute Online Courses on Complexity]==		'''[http://www.complexityexplorer.org/online-courses Santa Fe Institute Online Courses on Complexity]'''<br>
	==[https://www.youtube.com/user/santafeinst A huge online archive of Santa Fe Institute YouTube Videos]==		'''[https://www.youtube.com/user/santafeinst A huge online archive of Santa Fe Institute YouTube Videos]'''<br>
	==[http://www.complexityexplorer.org/explore/resources Background Reading on Complexity]==		'''[http://www.complexityexplorer.org/explore/resources Background Reading on Complexity]'''<br>
	==[http://tuvalu.santafe.edu/projects/musicplusmath/ Music + Math Website!]==		'''[http://tuvalu.santafe.edu/projects/musicplusmath/ Music + Math Website!]'''<br>

	===General Agent-Based Modeling===		===General Agent-Based Modeling===

Juniperlovato at 14:52, 15 July 2014

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	==Readings and Materials==		==Readings and Materials==

			===Resources===

			==[http://fractalfoundation.org/ Fractal Foundation]==
			==[http://santafe.edu/ Santa Fe Institute Website]==
			==[http://www.complexityexplorer.org/online-courses/11 Introduction to Complexity Online Videos]==
			==[http://www.complexityexplorer.org/explore/glossary Complexity Explorer Terms Glossary]==
			==[http://www.complexityexplorer.org/online-courses Santa Fe Institute Online Courses on Complexity]==
			==[https://www.youtube.com/user/santafeinst A huge online archive of Santa Fe Institute YouTube Videos]==
			==[http://www.complexityexplorer.org/explore/resources Background Reading on Complexity]==
			==[http://tuvalu.santafe.edu/projects/musicplusmath/ Music + Math Website!]==

	===General Agent-Based Modeling===		===General Agent-Based Modeling===

Juniperlovato at 21:09, 20 August 2013

2013-08-20T21:09:53Z

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	[[Image: SFIcamp20143.jpg]]		[[Image: SFIcamp20143.jpg]]

			==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]

Juniperlovato at 20:55, 20 August 2013

2013-08-20T20:55:57Z

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			[[Image: SFIcamp20143.jpg]]

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