CSSS 2008 Santa Fe-Readings

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CSSS Santa Fe 2008

Week One: Modeling/Nonlinear Dynamics

Liz Bradley: Non-Linear Dynamics I-IV

Nonlinear Dynamics

Owen Densmore & Steve Guerin: Modeling

Before the modeling class (afternoon the first day!) you should:

  • Download the most recent versions of both NetLogo and NetLogo 3D from
  • Run some of the Model Library examples for both NetLogo and NetLogo 3D:
    • Start the application
      • Click Model Library in the File menu, try these:
      • NetLogo: Art > Diffusion Graphics
      • NetLogo 3D: 3D > Sample Models > Raindrops 3D
        Note: move the 3D raindrop world by click & drag
      • To run most of the models, click "Setup" then "Go"
      • To see the code, click on the Procedures tab
  • Finally, under the "Help" menu, click "User Manual" and explore!

Week Two: Ecology/Evolution/Molecular Biology/Disordered Systems

Aaron Clauset: MCMC for Simulation and Inference

The following three references cover a wide variety of details related to Markov chain Monte Carlo (MCMC) methods. The second and third are general references, written for physics and machine learning audiences. (The Newman and Barkema book should be available through the SFI Library.) The first shows an application of MCMC methods in the context of learning the large-scale structure of networks.