Notes and Software for Artificial Life (M.Sc.)

Slides from Robotics Tutorial by Dr. Joe Saunders: week 1

• Introduction to AI Robotics by Robin Murphy (MIT Press, 2001).
  
• Behavior-based Robotics by Ronald C. Arkin (MIT Press, 1998).

Cellular Automata

1. Golly, a cross-platform system supporting Conway's Game of LIfe and other Cellular Automata, including the von Neumann self-replicator.
   
2. Self-Replication loops in Cellular Space: Byl, Langton, Chou/Reggia, and Sayama self-replicating loops.
3. Source Code for William Flake's book The Computational Beauty of Nature (MIT Press, 2000): http://mitpress.mit.edu/books/FLAOH/cbnhtml/source.html
   See "ca" for Cellular Automata, "hp" for Hodge-Podge Machine.

Swarm Intelligence

EVOLUTION

COMPUTATIONAL MORPHOGENESIS

L-Systems:
L-Systems Tutorial and L-Parser Software
The Algorithmic Beauty of Plants book on-line, P. Prusinkiewicz and A. Lindenmayer (Springer, 1990).

Diffusion-Reaction Systems:

Hans Meinhardt's webpage and demo programs

Modelling Biological Pattern Formation book on-line by Hans Meinhardt (Academic Press, 1982).

Morphogenesis of Cellular Slime Mould Dictyostelium discoideum using 2-layer Glazier-Graner CA model and underlying excitable medium) by Stan Marée. See his PhD thesis From Pattern Formation to Morphogenesis (Utrecht Univ., 2000)

EVOLUTIONARY COMPUTATION

Thinking through the tutorial will help you understand GAs with some concrete examples in applets, including the travelling salesman problem and some examples of GA encodings ("representation problem" -- tree encodings illustrated in the tutorial are used in Genetic Programming). Some of the applets let you can set different kinds of crossover, mutation and selection operators, and different mutation and crossover rates. Have Fun!

• The "genesis" program (by J. J. Grefenstette) for a genetic algorithm (GA) operating on fixed-length character strings is here: genesis.tar .
• documentation, installation instructions, and examples: [genesis.txt] [genesis.ps]

  This is Genetic Algorithm engine in C that compiles under unix/linux (maybe other systems). Documentation is in genesis.txt. You can write your own function in C to compute fitness and use genesis to setup the GA and parameters, run it, logging performance information (see documentation for examples).

• Tierra Documentation Version IV.10 [ASCII text file]: detailed instructions on how to install and run tierra, compile and disassemble tierra virtual code, etc.
• Tierra Software Version IV.10 (version discussed in article and lecture) source code
  [tar archive]
  This compiles in tierra subdirectory, with "make programs", this archive incluces linux binaries for Redhat:
  tierra1 (tierra), to arg1 (compile or disassemble tierran entitities)]
  Here is the same tar archive without binaries: [tar archive w/o binaries]. This should be compilable on many platforms, but you may have to edit the Makefile.
• For windows, the original version we pointed you to might not run on Windows machines, sometimes with flicker or other problems in Win2000 and Win98, (WinXP? Windows7?). For anyone wanting to do a project with Tierra we recommend you download source code and get it to compile on your machine.

  Windows Executable Tierra VersionV.0 from : [tar archive]

• Tierra Version 6.02 source code and executables, and the Tierra video, are at the tierra homepage http://life.ou.edu/tierra/
  We have not used version 6. Version 5 does not include adequate documention, but the documentation for version IV.10 (see above to download) should help. Note that for a project you probably want "NonNet Tierra" rather than "Net Tierra". Net Tierra is used for running multiplie tierra virtual OS's on multiple machines between which creatures can migrate.

1. NetTeirra:
   1. Ray, T. S. 1998. Selecting Naturally for Differentiation: preliminary evolutionary results. Complexity, 3(5): 25-33. John Wiley & Sons, Inc.
      [PDF at publisher (153 K)]
   2. Ray, T. S. and Joseph Hart. 1998 Evolution of Differentiated Multi-threaded Digital Organisms. In: Artificial Life VI proceedings, C. Adami, R. K. Belew, H. Kitano, and C. E. Taylor [eds.], 295-304. The MIT Press, Cambridge. Download entire document in MSWord format.
2. Origins of Differentiated Multicellularity and Evolutionary Transitions in Individuality
   Sept 2005, EEB Noon Seminar, Tucson. Life History Evolution and the Origin of Multicellularity by Richard E. Michod