BY659/CS659
FALL 2008

Lecturer: James F. Lynch
Office: SC-381
Telephone: 268-2374
email: jlynch@clarkson.edu
Office hours: MW 9:00AM–10:00PM, MW 11:00AM–12:00PM
Lecture hours: M 2:30PM–3:45PM, F 8:30AM–9:45AM, SC–336
Text: This will depend on the interests of the class.  We may choose one book, in which case I would expect all students to get a copy of it, or we may read selections from a wide variety of sources, including books and journal articles that I would post online.  I’ll bring examples of books and articles to our first meetings.

GRADING

Grading will be based entirely on the readings and participation in discussions and experiments with software. There may be some problems assigned as homework, but there will be no exams or final.

READING

Jeremy M. Berg, John L. Tymoczko, and Lubert Stryker, Biochemistry, 5th Ed., W, H, Freeman and Company, New York (2002), Chapter 1, pp. 3-18.

Jeremy M. Berg, John L. Tymoczko, and Lubert Stryker, Biochemistry, 5th Ed., W, H, Freeman and Company, New York (2002), Chapter 2, pp. 19-40.

Steven Levy, The Promised Land, in Artificial Life, Pantheon Books, New York (1992), pp. 11-46.

Steven Levy, Playing by the Rules, in Artificial Life, Pantheon Books, New York (1992), pp. 47-83.

Steven Levy, Garage-Band Science, in Artificial Life, Pantheon Books, New York (1992), pp. 85-120.

Steven Levy, God's Heart, in Artificial Life, Pantheon Books, New York (1992), pp. 121-152.

Zhiqiang Liu, Quorum Sensing, pdf slides.

Robert Hillborn, A simple model for stochastic coherence and stochastic resonance, Am. J. Phys. 72 (2004), pp. 528–533.

Frederick K Balagaddé et al., A synthetic Escherichia coli predator-prey ecosystem, Molecular Systems Biology 4:187, published online (2008).

Arthur W. Burks, Von Neumann’s Self-Reproducing Automata, in Essays on Cellular Automata, ed. A. W. Burks, University of Illinois Press, Urbana (1970), pp. 3-64.

Zhiqiang Liu, Von Neumann Cellular Automaton, ppt slides

Shruti Parihar, Self Reproducing Cellular Automata and Programs

S. Di Gregorio et al., Applying cellular automata to complex environmental problems:  The simulation of the bioremediation of contaminated soils, Theoretical Computer Science 217 (1999), pp. 131–156.

Class discussion of bioremediation

Zhiqiang Liu, Second and Third Layers of Bioremediation CA

Steven Levy, The Genetic Algorithm, in Artificial Life, Pantheon Books, New York (1992), pp. 153-187.

Application of Genetic Algorithm

FAQ: What’s a Genetic Algorithm?

Genetic Algorithms

Genetic algorithm - Wikipedia

Introduction to Genetic Algorithms

The Caml Hump:  GenePool

Pat Wilburn, C++ implementation of GA for Hello World!

Zne-Jung Lee, A novel hybrid algorithm for function approximation

Kawalpreet Kaur, Applying Multi-Objectice Genetic Algorithms in Green Building Design Optimization

Thiemo Krink, Swarm Intelligence - Introduction

Mark Fleischer, Foundations of swarm intelligence: from principles to practice

Eric Bonabeau, Swarm intelligence, Proc. Emerging Technology Conf., (2003)

Peter Miller, Swarm theory, National Geographic Magazine online, July (2007)

Leandro Nunes de Castro, Swarm Intelligence, in Fundamentals of Natural Computing, Chapman & Hall/CRC, Boca Raton, FL (2006), pp. 205–266.

Zhiqiang, Liu, Particle Swarm Optimization

 

QUESTIONS FOR DISCUSSION

Monday, September 1
Friday, September 5
Friday, September 26
Friday, October 3
Monday, October 13

LINKS

Alife

Conferences and Workshops

Corporations

Research Groups and Institutes

Software

QUOTES

  • Biologists can be divided into two classes: experimentalists who observe things that cannot be explained, and theoreticians who explain things that cannot be observed. - Aharon Katzir-Katchalsky
  • [Ask] not what mathematics can do for biology but what biology can do for mathematics. - Stanislaw M. Ulam, paraphrasing a famous remark of John F. Kennedy