Complex Systems Summer SChool 2013-Lecture Readings

Complex Systems Summer School 2013 Home Research Assistant Position Details Surveys/Evaluations Logistics Faculty Participants Schedule Lecture Slides Background Readings Software Projects & Working Groups CIB Markov Comedy and Tragedy in Shakespeare Global Emergent Risk NetAttac Cities Matrix Matters Synchrony on Networks Unfolding History Tutorials Blog Glue Session Forum Project Presentations Final Papers After Hours Hiking Photos TShirts Question Of the Week Page

Sander Bais

Symmetries Lecture

Liz Bradley

Slides

Syllabus
Lecture 1 (Introduction to Nonlinear Dynamics, Maps)
Lecture2 (Flows) Complete Slides

Notes

Time Series Analysis
Numerical Solution of Differential Equations

Aaron Clauset

Lectures 1-2: http://bit.ly/14uNw3N
Lecture 3: http://bit.ly/19DBuZj
Lecture 4: http://bit.ly/10mgYJZ

Jim Crutchfield

The Complexity lecture PDFs (2) are here:

Complexity Lecture Slides 1
Complexity Lecture Slides 2

Interactive HTML versions (with all animations) are here:

Complexity Lecture Slides 1
Complexity Lecture Slides 2

Jennifer Dunne

Ecological Network Structure & Dynamics Lecture Slides

Jessica Flack

Papers and books of interest in the robustness literature

John Harte

John Harte Slides

Alfred Hubler

Talk 1
Talk 2
Lab Manual

Melanie Mitchell

Slides

Lecture 1, Biologically Inspired Computing
Lecture 2, Simple models of self-organization and emergence
Video: What are Complex Systems?

NetLogo Files

Ants
Fireflies
Flocking
Preferential Attachment
Robby the Robot GA's

Mercedes Pascual

Slides

Lecture 1, Macroscopic patterns in pathogen diversity form an ecological perspective
Lecture 2, Anticipating critical transitions

Additional Reading

Canalization of the evolutionary trajectory of the human influenza virus- Trevor Bedford, Andrew Rambaut, and Mercedes Pascual
Quantifying limits to detection of early warning for critical transitions -Carl Boettiger and Alan Hastings
From patterns to predictions - Carl Boettiger and Alan Hastings
Robust scaling in ecosystems and the meltdown of patch size distributions before extinction - Sonia Kefi, Max Rietkerk, Manojit Roy, Alain Franc, Peter C. de Ruiter, and Mercedes Pascual
Forecasting a class of bifurcations: Theory and experiment - Joosup Lim and Bogdan I. Epureanu
ALTERNATIVE STABLE STATES IN EUTROPHIC, SHALLOW FRESHWATER SYSTEMS: A MINIMAL MODEL - M. SCHEFFER
Early-warning signals for critical transitions - Marten Scheffer et al.
Epochal Evolution Shapes the Phylodynamics of Interpandemic Influenza A (H3N2) in Humans - Katia Koelle et al.
Anticipating Critical Transitions - Marten Scheffer et al
Appendix: Slow Recovery from Perturbations as a Generic Indicator of a Nearby Catastrophic Shift - E. H. van Nes and M. Scheffer
Slow Recovery from Perturbations as a Generic Indicator of a Nearby Catastrophic Shift. - Egbert H. van Nes and Marten Scheffer
Understanding Shifts in Wildfire Regimes as Emergent Threshold Phenomena. - Richard D. Zinck, Mercedes Pascual, and Volker Grimm
The Roles of Competition and Mutation in Shaping Antigenic and Genetic Diversity in Influenza - Daniel Zinder, Trevor Bedford, Sunetra Gupta, Mercedes Pascual

Cris Moore

Quantum Computing
Phase Transitions
Algorithms and Landscapes

Cosma Shalizi

Lecture 1

Lecture 2

Advanced Data Analysis

Advanced Data Analysis from an Elementary Point of View

Syllabus with Slides

Andreas Wagner

Lecture Slides, Evolution and genotype networks

Simon DeDeo

References and Bibliography for Emergence and Reductionism talks