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2015 Complexity and Modeling Program Readings: Difference between revisions

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<!-- [[Media:Gajardo,_Moreira,_Goles_-_Complexity_of_Langton's_Ant.pdf | Complexity of Langton's Ant - Gajardo, Moreira, and Goles]] -->
<!-- [[Media:Gajardo,_Moreira,_Goles_-_Complexity_of_Langton's_Ant.pdf | Complexity of Langton's Ant - Gajardo, Moreira, and Goles]] -->
===Probability Puzzles===
Puzzle #1 [[Media:UnfairCoin.pdf | The Unfair Coin]]‎
Puzzle #2 [[Media:ProblemofPoints.pdf | Problem of points]]‎
Puzzle #3 [[Media:ProbabilityPuzzles.pdf | Dice Exercises]]‎


===Ecological Modeling===
===Ecological Modeling===
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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.]]‎  
[[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]]


[[Media:Kircher_-_Emergent_Behavior_of_Rock-Paper-Scissors_Game.pdf‎ | Emergent Behavior of Rock Paper Scissors - Kircher]]
[[Media:Bennett - Rock Paper Scissors.pdf | Rock-Paper-Scissors Ecosystem]]


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<!-- [[Media:Dunne_-_Encyclopedia_of_Complex_Systems,_Food_Webs.pdf | Food Webs - Dunne]] -->
<!-- [[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 ====
====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===
===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==
==Curriculum & Tools==
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[[Media:C1-Swords&Shields.doc‎ | Swords & Shields (doc)]]
[[Media:C1-Swords&Shields.doc‎ | Swords & Shields (doc)]]
[[Media:coreconcepts.pdf | Core Concepts (doc)]]
[[Media:langstonsants.pdf | Langston's Ants (doc)]]


==Suggested Readings==  
==Suggested Readings==  

Latest revision as of 23:25, 15 July 2015

2015 Complexity and Modeling Program Navigation


Readings and Materials

Santa Fe Institute Website

Complexity Resources

Introduction to Complexity Online Videos
Complexity Explorer Terms Glossary
Santa Fe Institute Online Courses on Complexity
A huge online archive of Santa Fe Institute YouTube Videos
Background Reading on Complexity

General Agent-Based Modeling

Probability Puzzles

Puzzle #1 The Unfair Coin‎

Puzzle #2 Problem of points‎

Puzzle #3 Dice Exercises‎

Ecological Modeling

Rock, Paper, Scissors

Rock Paper Scissors in Bacteria & Biodiversity - Kerr et al.‎

Emergent Behavior of Rock Paper Scissors - Kircher

Rock-Paper-Scissors Ecosystem


Chaos Theory

Deterministic Nonperiodic Flow - Lorenz‎

Networks

Epidemiology

Curriculum & Tools

Walk & Turn (doc)‎

Swords & Shields (doc)

Core Concepts (doc)

Langston's Ants (doc)

Suggested Readings

Why Model? - Joshua M Epstein,

Jim Crutchfield, The Dreams of Theory

Melanie Mitchell, Complexity: A Guided Tour

Thomas D. Seeley, Honey Bee Democracy

Suggested Videos

Video Catalog of SFI Lectures

Iain Couzin, Understanding Human Behavior

Hunting the Hidden Dimension, NOVA documentary on fractal geometry

Emergence, Abridged NOVA ScienceNOW documentary on emergent phenomena

Progect GUTS Intro to Complex Adaptive Systems

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