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CSCS 530 - January Syllabus

Jan 7 Wedn

First Class -- organizational meeting.
Brief description of course; administrivia.
Handouts / Items covered:

• Class0-Notes
• On Rigor in Science, by Jorges Borges.
• The antikythera Mechanism, a really old model! (The birth of science?)
• Past term projects

Things to read before next class:

• Excerpts from T. Schellings Micromotives and Macrobehavior, describing his "tipping" model of segregation.
• pp1-6 from Nino Boccara's book "Modeling Complex Systems," including a quote from John Maynard Smith on the difference between modeling and simulation.
• pp 1-8 of Agent-Based Models, Nigel Gilbert.
• pp 35-43 ("Modeling"), Complex Adaptive Systems, John Miller and Scott Page.
• Agent Based Models. Scott Page (2005). To appear in The New Palgrave Dictionary of Economics.

Optional readings (will re-read some later):

• Agent-based models. Dan Brown (2006)
  In H. Geist, Ed. The Earth’s Changing Land: An Encyclopedia of Land-Use and Land-Cover Change.
  Westport CT: Greenwood Publishing Group, pp.7-13.
• pp 57-77 of Complex Adaptive Systems, John Miller and Scott Page.
• Elizabeth Bruch and Mare, R.D. Neighborhood Choice and neighborhood change.
  American J. Sociology 112(4): 667-709 (2006).
• Sander,R., Schreiber,D. and J.Doherty. Empirically Testing a Computatonal Model: The Example of Housing Segregation. March 2000.

Jan 9 Fri

Agenda:

• Quick look at past term projects (to get you thinking)
• Demos of some "classic" ABM's (and others...)
• Discuss any questions regarding the readings assigned for this class (see Jan 7, above). We will fully discuss the general ABM readings on Jan 21.
• New CSCS computer users get started a bit at the consoles.

Handouts for today (or pages to read as needed):

• Past term projects -- handed out last class
• Demo script
• Heatbugs conceptual model
• Some starting linux hints
• Working in Linux -- most common commands, etc

Handouts for next class -- please read/scan:

• TermitesWoodchipsModelDescription
• High level view of java programs
• Java Short Summary -- two pages!
• Another summary of java programs and writing ABMs (Mostly the same as the above 2...)

First programs for next time -- take a look if you can:

• SimpleTermites programs -- how to get copies

Jan 14 Wed

Agenda:

• Start a fast introduction to Java.
• Collectively (or individually!) write the Termites-WoodChips model.

Handouts / Pages to read:

• See handouts from last class Jan 9
• Handed out today: SimpleTermites1/Main.java Model.java Termite.java
• Exercises to do (see below, Assignment).

Readings: Begin reading in your favorite Java Introduction about

• Whatever "Hello World" example the intro has!
• Variables, data types
• Expressions
• Conditional execution
• Iteration -- while, for loops
• Classes -- fields, methods; Define classes; use classes

You might want to read these "stories" from the Java Ranch:

• Variables -- primitives and reference
• Passing by value to methods

Assignment:

• Assignment -- ungraded, but critical that you do them!

Jan 16 Fri

Agenda:

• Finish going through the SimpleTermites program.
• Go through the SimpleTermites1 program.

Handouts:

• See last class
• SimpleTermites1/Model.java
• SimpleTermites1-Pic

Assignments:

• Finish the assignment from last class

Jan 21 Wed

Agenda:

• Discuss readings -- What are / Why use ABM?
• Discuss all course assignments:
  • Project #1 (Project1Groups)
  • Project #2
  • Short Paper
  • Term Project

Discussion Leaders: Marielle, Meghan, Trevor

Review/Re-Read required readings from early this term:

• pp1-6 from Nino Boccara's book "Modeling Complex Systems," including a quote from John Maynard Smith on the difference between modeling and simulation.
• Agent Based Models. Scott Page (2007). To appear in The New Palgrave Dictionary of Economics.
• pp 1-8 of Agent-Based Models, Nigel Gilbert.
• pp 35-43, 57-77 of Complex Adaptive Systems, John Miller and Scott Page.

New required readings:

• Joshua Epstein? "Why Model?" JASSS Vol 11 (4).
• Steven C. Bankes ."Agent-based modeling: A revolution?"
  PNAS 2002 99 (Suppl. 3): 7199-7200
• Grimm and Railsback. Chapter 1, Why IBM?
  from their book Individual-based Modeling and Ecology.
• Eason, Robb etal. What kind of science is simulation? Journal of Experimental & Theoretical Artificial Intelligence 19 (1): 19-28 (2007).
  Another version of this article (read if we can't get the one above):
  "The Science in Simulation: Structure and evaluation." (pdf of scan)
• Chap 7 of Complex Adaptive Systems, John Miller and Scott Page.
• Eric Bonabeau. "Agent-based modeling: Methods and techniques for simulating human systems."
  PNAS 2002 99 Suppl. 3: 7280-7287
• Di Paolo, Nobe and Bullock. "Simulation Models as Opaque Thought Experiments."
  (Postscript Version or PDF Version) Artificial Life VII: The Seventh International Conference on the Simulation and Synthesis of Living Systems, August, 2000.

Optional Readings:

Pick at least a couple articles from a list of optional readings to read, and then post some comments/questions to c-tools (best) or bring up comments/questions in class. There is a long list here, so pick out articles that are of interest to you (e.g., in your area, or just sound interesting).

Jan 23 Fri

Agenda:

• Finish SimpleTermites (from last class)
• Start on the TermitesInGrid program

Handouts:

• Notes from the TermitesInGrid program pages.
• Listing of the Model.java, Termite.java, GridWorld.java files.
• Three pictures of TermitesInGrid
• HowToAddParametersToModel
• HowToAddClassToModel
• NotesOnChangingAModel
• HowToAddAPlot, i.e., a Repast OpenSequenceGraph,
  and how to add a line to an existing plot. (Handed out last class)
• Assignments for TinG

Assignment:

• Get copy of TermitesInGrid program, compile, run a bit.
• Read through the TermiteInGrid "conceptual model" classes:
  Model.java, Termite.java, GridWorld
• Read/scan the Repast docs listed below
• If you can;
  • Read the HowTo/Notes docs listed for [[28 Jan -> #Jan28]
  • Get a start on TermitesInGridAssignment1 (also listed under 28 Jan)

Readings:

• Please read/scan the Repast 3.x HowTo documentation pages, in particular these:
  • How to run a simulation: commands for running repast on a windows machine.
    You can do similar things under linux (eg at CSCS), but you do have to change\\ the paths accordingly. See this page for how to run the basic Repast on cscs machines.
  • How to use the GUI: Describes the buttons, etc, in (most) Repast programs
  • How to Build a Model-1: just scan this one.
  • How to Build a Model-2: The models we build will start with the class SimModelImpl, described in this.

Read the other Repast-HowTo pages that interest you (e.g., regarding networks).

Jan 28 Wed

Agenda:

• Finish TermitesInGrid
• Briefly discuss TermitesInGrid1 and TermitesInGrid2 assignment.
  My notes on doing the assignment are here
• Discuss the use of "cast" operator, and use of getClass() to get an objects class.
  See /users/rlr/Courses/530/Src/Test/TermintesInGrid2 Termite.java testCasts() method.
  Note: TermitesInGrid2 has a solution to the TermitesInGrid assignments,

  so don't look until you have tried to do those exercises.
• Start on AntPheromones1 -- the starting place for project #1.

Handouts / Things to read:

• AntPheromones1-Readme-GetCopy
• Sketch of model, world and pheromone space (pdf)
• Extracts from Model,Bug,GUIModel classes
• SynchronousUpdating (pdf)
• Notes on the ColorMap for displaying pheromone

Assignment for practice from TermiteInGrid:

• TermitesInGridAssignment1 -- add WoodChip class; add wood chips to world
• TermitesinGridAssignment2 -- change so termites pick-up/put-down chips.

Assignment for next class:

• Read over the AntPheromones1 Model and Bug java files.
• AntPheromones1Assignment -- get started on it if you can

Jan 30 Fri

Agenda:

• Finish TermitesInGrid
• Start looking at AntPheromones1 (see handouts from last class)

Handouts / Things to read:

• The TermitesInGrid/GUIModel.java file
• Notes on using jar (save.sh) to save program snapshots

Assignment:

• Read over the AntPheromones1 Model and Termite java files.
• Try AntPheromones1Assignment -- as much as you can.

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