Education

Course Offerings - CSCS (Division 348) 530

CSCS 530 -- Readings

Under construction for Winter 2006

Last Changed: 28 Oct 2005

This is a list of books, papers and online resources that are relevant to CSCS-530.

Re. the books:
A few readings will be assigned from sections of the books, or will have sections as optional readings. The books will either be on reserve, or copies of short sections will be distributed, so you don't need to buy all these. (However, many are very interesting and generally useful....)

Re. the papers:
This is a tentative list of papers we will be reading for each of the listed topics. In some cases we will only read a selection of the papers listed, while for some topics different papers may be added or substituted.

Note: Papers to be read will be distributed in course packs, from AccuCopy (the place on William, next to Cottage Inn).

Papers

Agent-Based, Bottom-Up, Exploratory Modeling


New Computer Models Unify Ecological Theory.
  Huston, Michael, DeAngelis, Donald and Post, Wilfred.
  BioScience, 38(10), 682-691 (1988).


The Rise of the Individual-based model in ecology.
  Judson, Olivia P.
  Trends in Ecol. and Evol, 9(1), 9-14 (1994).


New Computer Architectures as Tools for Ecological Thought.
  Villa, Fernando.
  Trends in Ecol. and Evol, 7(6), 179-183 (1992).


Exploratory Modeling for Policy Analysis.
  Bankes, Steve.
  Operations Research, 41(3), 435-449.  1994.


Validation of Exploratory Modeling.
  Bankes, Steve and Gillogly, James.
  Proc. Conf on High Performance Computing, pp382-387. 1994.
  A.M. Tentner and R.L. Stevens (eds).


Adaptive Computation in Ecology and Evolution: 
  A Guide to Future Research.
  J. Roughgarden etal, pages 25-30 of 
  Adaptive Individuals in an Evolving Population.


Computation and the Natural Sciences.
  R.K. Belew etal, pages 431-440 of 
  Adaptive Individuals in an Evolving Population.


Agent-Based Modeling vs. Equation-Based Modeling: A Case Study and Users' Guide.
Parunak, H. Van Dyke, Savit, Robert and Riolo, Rick.
Proceedings of Workshop on Multi-agent systems and Agent-based
Simulation (MABS'98), Springer, 1998.


Validation, Verification


Active Nonlinear Tests (ANTs) of Complex Simulation Models.
  Miller, John.
  Sante Fe Institute Working Paper 96-03-011.


Agent-Based Modeling: Understanding Our Creations.
  From SFI Bulletin, Winter 1994.
  Axtell, Robert and Epstein, Joshua.


Aligning Simulation Models: A Case Study and Results
  Axtell, Robert, Axelrod, Robert, Epstein, Joshua, and Cohen, Michael.
  SFI Working Paper 95-07-065.


Exploratory Modeling.  Search Through Spaces of Computational Experiments.
  Bankes, Steve.
  Proc. Third. Conf on Evolutionary Programming, pp353-360. 1994.

 
A Tutorial on Validation and Verification of Simulation Models.
  Sargent, Robert G.
  Proc. of 1988 Winter Simulation Conference, pp33-39.
  M. Abrams, P. Haigh and J. Comfort (eds).

Things that can go bump in the night


Evolutionary games and spatial chaos.
  Nowak, Martin and May, R.M.
  Nature, 359, pp826-929.


Evolutionary Games and Computer Simulations.
  Huberman, Bernardo A. and Glance, Natalie S.
  Proc. Natl. Acad. Sciences (USA), 90, 7716-18 (1993).


Spatial games and the maintenace of cooperation.
  Nowak, Martin, Bonhoeffer, S. and May, R.M.
  PNAS (USA), v91, pp4877-4881.  1994.


Monte Carlo Simulations: Hidden Errors from 'Good' Random Number Generators.
  Ferrenberg, Alan M., Landau, D.P., and Wong, Y.Joanna.
  Physical Review Letters 69(23).   Dec 1992.
  See also News and Views in Nature Vol 372, 1 Dec 1994.


Rediscovering Computational Autopoiesis.
  McMullin, Barry, and Varela, Francisco J.  (1997)
  SFI Working Paper 97-02-012.


Validating Models of Ecosystem Response to Global Change.
Edward B. Rastetter.
Bioscience, v46 (3), p190-198.

Interaction Topology


The Localisation of Interaction and Learning in the
          Repeated Prisoner's Dilemma.
  Hoffmann, Robert and Waring, Nigel.
  SFI Working Paper 96-09-xx.


How Topology Affects Population Dynamics.
  Kephart, Jeffrey O.
  Artificial Life III, 447-463.  Langton (ed). 1994.


Zones of Cooperation.
  Epstein, Joshua M.
  Originally SFI Worling paper SFI-98-XX-XXX.
  Also in Complexity, Volume 4, Issue 2, 1998, pp36-48  
  Zones of cooperation in demographic prisoner's dilemma


  

The effects of tag-mediated selection of partners in 
       evolving populations playing the Prisoner's Dilemma.
  Riolo, Rick L.
  Proc of 7th Intern. Conf on Genetic Algorithms, pp378-385. 
  Thomas Back (ed); Morgan Kaufmann.


Watts, Duncan and Strogatz, Steven H.
Collective dynamics of 'small-world' networks.
Nature, v393, 440-443. 1998.

Emergence


Evolving Cellular Automata to Perform Computations:
  Mechanisms and Impediments.
  Mitchell, M., Crutchfield, J.P. and Hraber, P.T.
  SFI Working Paper 93-11-071. (Also submitted to Phsysica D.)


Embedded-Particle Computation in Evolved Cellular Automata.
  Wim Hordijk, James P. Crutchfield, and Melanie Mitchell.
  SFI Working Paper 96-09-073.
  (To appear in Physics and Computation 96.)

Is Anything Ever New?  Considering Emergence.
  Crutchfield, James P.
  SFI Working Paper 94-03-011.


The Barrier of Objects:  From Dynamical Systems to Bounded Organizations.
  Fontana, Walter, and Buss, Leo W.
  SFI Working Paper 96-xx-xx.


Beyond Digital Naturalism.
  Fontana, Walter, Wagner, Gunter, and Buss, Leo W.
  Artificial Life, vol 1-2. (1994).

Studying Artificial Life Using a Simple, General Cellular Model.
  Sipper, Moshe.
  Artificial Life, 2 (1), pp1-35.  1995.

An Evolutionary Approach to Synthetic Biology.
  Ray, Tom. S.
  Artificial Life, 1(1), 1994.


Evolution as a self-organized critical phenomenon.
  Sneppen, Kim, Bak, Per, Flyvbjerg, Henrik and Jensen, Mogens H.
  PNAS USA vol 92, pp5209-5213. (1995).


Criticality and Scaling in Evolutionary Biology.
  Sole, Ricard V. Manrubia, Susanna C., Benton, Michael,
     Kauffman, Stewart and Bak, Per.
  Submitted to Trend in Ecology and Evolution (TREE).


Avalanches, Scaling and Coherent Noise.
  Newman, M. E. J. and Sneppen, Kim.
  LANL E-Print cond-mat/9606066.


A Breakthrough Book? Review of How Nature Works.
  David M. Raup.
  Complexity, Vol 2 (6), p30-33. (1997).


Is the Geometry of Nature Fractal?
  Avnir, David etal.
  Science, vol 279, 2 Jan 1998.

Social Systems


The Convergence and Stability of Cultures.
  Axelrod, Robert.
  SFI Working Paper 95-03-028.


A Self-Forming Neighborhood Model
  Schelling, Thomas C.
  Pp 147-165 of his book "Micromotives and Macrobehaviors."

Dynamic Models of Segregration.
  Schelling, Thomas C.
  J. Math. Sociology, 1, pp143-186.  1973.
  Optional.


Measuring Emergent Social Phenomena: Dynamism Polarization,
  and Clustering as Order Parameters of Social Systems.
  Latane, Bibb, Nowak, Adrzej and Liu, James H.  (1994)
  Behavioral Science, v39, pp1-24.

Social dilemmas exist in space.
  Nowak, Adrzej, Latane, Bibb and Lewenstein, Maciej. (1994)
  Pp 269-289 in Social Dilemmas and Cooperation.
  Schulz, U., Ablers, W. and Mueller, U. (eds).   Springer-Verlag.

Clustering processes in economic transition.
  Nowak, Adrzej, Urbaniak, Jakub and Zienkowski, Leszek. (1996)
  Pp 42-61.

Modeling Social Change with Cellular Automata.
   Nowak, Andrzej and Lewenstein, Maciej.  (1996)
   Pp 249-285 in Modeling and Simulation in the Social Sciences
   from a Philosophical Pint of View.
   Hegselmann etal., eds.  Kluwer, Boston.


Ecological Systems


Foraging in Flocks: non-spatial models may neglect important costs.
  Ruxtom, G. D.
  Ecological Modelling, 82, pp277-285.  1995.


Spatial self-organization in ecology: pretty patterns or robust reality?
  Trends in Ecol. and Evolution (TREE), v12(2), pp70-74.
  Rohani, P., Lewis, T.J., Grunbaum, D, and Ruxton, G.D. (1997)


Evolution in an Individual-Based Model Alters
  Population Dynamics and Community Structure.
  Hartvigsen, G. and Levin, S.A. (in review for Science, 1997)


Dynamics of Age-Structured and Spatially Structured Predator-Prey
      Interactions: Individual-Based Models and Population-Level Formulations.
  McCauley, Edward, Wilson, William G. and deRoos, Andre M.
  The American Naturalist, 142(3), pp412-442.  1993.


 Resolving Differences between Deterministic Population
         Models and Individual-Based Simulations.
 Wilson, William G.
 The American Naturalist, vol 151 (2), pp116-134.
 

The Consequences of stochasticity for self-organized spatial dynamics,
     persistence and coexistence in spatially extended
     host-parasitoid communities.
  Ruxton, Graemed D. and Rohani, Pejman.
  Proc R. Soc. B, v263, pp625-631 (1996).


Evolutionary consequences of spiral waves in host-parasitoid systems.
  Boerlijst, M.C., Lamers, M.E. and Hogeweg, P.
  Proc. Royal Soc. London Series B, v253, pp 15-18 (1993)


Modeling food web complexity: the consequence of individual-based
     spatially explicit behavioral ecology on trophic interactions.
  Schmitz, Oswald J. and Booth, Ginger.
  Evolutionary Ecology (in Press).


Modelling coevolution in multispecies communities.
  Caldarelli, Guido, Higgs, Paug G. and McKane, Alan J.
  LANL E-Print archives adapt-org/9801003.

The Ecology of Echo.
  Jones, Terry, Hraber, Peter T. and Forrest, Stephanie.
  SFI Working Paper 96-07-xxx.
  Submitted to Artificial Life.

Gecko: A Continuous 2-D World for Ecological Modeling. (1997)
  Booth, Ginger.


The evolution of cooperation in an ecological context: an agent-based model.
Pepper, John and Smuts, Barbara.
To appear in "Dynamics of Human and Primate Societies: Agent-Based Modeling
  of Social and Spatial Processes."  
  Timothy A. Kohler and George J. Gumerman (eds.)
  Santa Fe Institute.  Oxford University Press, NY.  1999.


An individual-based model that reproduces natural distributions
        of species abundance and divserity.
Herraize, C.I., Merelo, J.J., Olmeda, S., and Prieto, A.

Economics


Readings from Epstein and Axtel's book, Growing Artificial Societies.


Decentralized, dispersed exchange without an auctioneer.
  Albin, Peter and Foley, Duncan K.
  J. Econ. Behav. and Organization 18, pp27-51.  1992.


Self-Organization of Markets: An Example of a Computational Approach.
  Vfriend, Nickolas.
  Computational Economics 8, pp205-231.

Sterman, John.
  Modeling Managerial Behavior: Misperceptions of Feedback in a Dynamic
       Decision Making Experiment.
  Sterman, John D.
  Management Science 35 (3), 321-339.  1989.


Asset Pricing Under Endogenous Expectations in an Artificial Stock Market.
  Arthur, W. Brian, Holland, John H., LeBaron, Blake, Palmer, Richard
    and Talyer, Paul.
  SFI Working Paper 1996-12-xx.


Inductive Reasoning and Bounded Rationality.
  Arthur, Brian W.
  Amer. Econ. Assoc. Papers and Proc. 84:406-411 (1994).


  Emergence of Cooperation and Organization in an Evolutionary Game.
  Challet, D.  and Zhang, Y. C.


Adaptive Competition, Market Efficiency, and Phase Transitions.
  Savit, Robert, Manuca, Radu and Riolo, Rick.
  .  Pre-print on PSCS web pages.


Seeing the Light at the El Farol.
  Casti, John L.
  Complexity, 1: 7-10 (1996).



Swarm Documents

Swarm and its documentation are available at the Santa Fe Institute
Swarm site.
On CSCS machines, see the

notes about Swarm at UM, including locations of
local copies of documentation, libraries and demos.
A few pointers to other papers about Swarm are also 
in the CSCS 530 Course outline.

There is a draft of a Swarm Users Guide, which you can
print on the CSCS machines by doing:
 
lpr ~rlr/swarm-userbook.ps
Its not complete, and needs more work, but it does
have some useful information.

Another paper:
The Swarm Simulation System and Individual-Based Modeling.
  Hiebeler, David. (1994.)
  Note: this describes an older version of Swarm, but much
        of the basic approach is still present.
  (It is in /s/Swarm/papers/swarm-sfi.ps and 3 swarm-fig*.ps files.)
  

Books 

Simulation

Simulation for the Social Scientist.
  Nigel Gilbert and Klaus G. Troitzsch.
  Open University Press, 1999.

Simulation model design and execution: building digital worlds
  Fishwick, Paul A.
  Englewood Cliffs, N.J. : Prentice Hall, 1995.
  On reserve (Media Union)?

Simulation modeling and analysis.
  Law, Averill M. and Kelton, W. David.
  New york : McGraw-Hill, 1991.  (2nd Edition)
  On reserve (Media Union)?

A guide to simulation.
  Bratley, Fox and Schrage.
  Springer, New York.  1987. (2nd edition)

Modeling Nature: Cellular Automata Simulations with Mathematica.
  Gaylord, Richard J. and Nishidate, Kazume.
  Springer Verlag, 1996.

Computer Programming

The CSCS Computer lab has 3-4 additional books that
are Introductions To C, and to Unix, and to the Make utility.


An Introduction to Object-Oriented Programming.
  Timonty Budd.
  Addison Wesley. 2nd Edition, 1998.
  This book is especially good, and it uses ObjectiveC
  (as well as Java and SmallTalk).

Code Complete. A Practical Handbook of Software Construction.
  Steve McConnell
  Microsoft Press. Redmond, Washington.  1993.

Design Patterns: elements of reusable object-oriented software.
  Gamma, Helm, Johnson and Vlissides.
  Reading, Mass. : Addison-Wesley, c1995.
  On reserve at (Media Union)?

Object-Oriented Programming and the Objective C Language.
  Nextstep.
  Its available online here, and you can order it from there 
  (go to the Documentation Index link in the upper left),
  and from bookstores.

Object-Oriented Methods: A Foundation.
  James Martin and James J. Odell.
  Prentice Hall, NJ.  1998.

C in Plain English.
  Brian Overland.
  MIS:Press, Henry Holt Pub, 1995.

Practical C Programming.
  Steve Oualine.
  O'Reilly & Associates, 1997.

C for Dummies. Volume 1.
  Dan Gookin.
  IDG Books, 1996.

The C Programming Language.
  Kernighan, Brian W. and Ritchie, Dennis M.
  Prentice Hall.  (Edition ?)

C: A Reference Manual.
  Harbison, Samuel P. and Steele, Guy L. Jr.
  Prentice Hall. (3rd edition at least)

Mathematica for Scientists and Engineers.
  Bahder, Thomas B.
  Addison Wesley. 1995.


General complex systems related books

Reality Rules: picturing the world in mathematics.
  Casti, J. L.
  New York : J. Wiley, c1992.


Would-Be Worlds: How Simulation is Changing the Frontiers of Science.
   Casti, John.
   Wiley, NY.  1997.
   Abbrev: WBW


Hidden Order: How Adaptation Builds Complexity.
   Holland, John H.
   The MIT Press, 1995.


Emergence: From Chaos to Order.
   Holland, John H.
   Addison Wesley, Reading MA. 1998.

Out of Control
  Kelly, Kevin.
  Addison Wesley.   1996.


How Nature Works: the science of self-organized criticality.
  Bok, Per.
  Springer-Verlag.  1996.


Growing Artificial Societies: Social Science From the Bottom Up.
   Epstein, Joshua M and Axtell, Robert.
   The MIT Press.  1996.
   Abbrev:  GAS


Adaptive Individuals in Evolving Populations.
  Ed. R. K. Belew and M. Mitchell.
  Vol XXVI of the SFI Studies in the Science of Complexity Series,
  Addison-Wesley, 1996.