BY659/CS659
FALL 2006

Lecturer: James F. Lynch
Office: SC-381
Telephone: 268-2374
email: jlynch@clarkson.edu
Office hours: TuTh 11:00AM-1:00PM and Wed 1:00PM-2:00PM
Lecture hours:TuTh 9:30AM-10:45AM, SC-342
Text: None

SYLLABUS

We will read and discuss a collection of articles from scientific journals and chapters from books. For the most part, we will all read each article and discuss it during class,although I may occasionally ask an individual student to give a lecture, and we may have some guest lecturers. In any event, I will require each student to turn in (by email or paper) a short report on each article before the class in which it will be discussed.

We may examine some systems biology software, and some students may develop software related to the course and report on it.

GRADING

Grading will be based entirely on the reports and participation in discussions and experiments with software. There will be no exams or final.

READINGS

  1. Steven Levy, The Promised Land, in Artificial Life, Pantheon Books, New York (1992), pp. 11-46.
  2. 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.
  3. W. Richard Stark and William H. Hughes, Asynchronous Irregular Automata Nets: The Path not Taken, BioSystems 55 (2000), pp. 107-117.
  4. Steven Levy, Playing by the Rules, in Artificial Life, Pantheon Books, New York (1992), pp. 47-83.
  5. Steven Levy, Garage-Band Science, in Artificial Life, Pantheon Books, New York (1992), pp. 85-120.
  6. Christopher G. Langton, Studying Artificial Life with Cellular Automata, Physica D 22 (1986), pp. 120-149.
  7. Christopher G. Langton, Computation at the Edge of Chaos: Phase Transitions and Emergent Computation, Physica D 42 (1990), pp. 12-37.
  8. Steven Levy, God's Heart, in Artificial Life, Pantheon Books, New York (1992), pp. 121-152.
  9. Stuart A. Kauffman, Antichaos and Adaptation, Scientific American (1991), pp. 78-84.
  10. James F. Lynch, Dynamics of Random Boolean Networks, Conference on Mathematical Biology and Dynamical Systems, The University of Texas at Tyler, October 7, 2005
  11. James F. Lynch, Dynamics of Random Boolean Networks, invited submission to Proceedings of Conference on Mathematical Biology and Dynamical Systems
  12. 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.
  13. 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.
  14. Dennis Bray, Protein Molecules as Computational Elements in Living Cells, Nature 376 (1995), pp. 307-312.
  15. U. Alon, Tutorial on E. Coli Chemotaxis; Robustness of the Chemotaxis Circuit.
  16. The Gillespie Algorithm, Rice University webpage.
  17. StochSim, University of Cambridge webpage.
  18. Thomas Simon Shimizu and Dennis Bray, Computational Cell Biology - The Stochastic Approach, in Foundations of Systems Biology, ed. H. Kitano, The MIT Press, Cambridge, MA (2001).
  19. Michael Huston, Donald DeAngeles, and Wilfred Post, New Computer Models Unify Ecological Theory, BioScience 38 (1988), pp. 682-691.
  20. Janusz Uchmański, David Aikman, Tomasz Wyszomirski, and Volker Grimm, Editorial: Individual-Based Modelling in Ecology, Ecological Modelling 115 (1999), pp. 109-110.
  21. Volker Grimm, Ten Years of Individual-Based Modelling in Ecology: What Have We Learned and What Could We Learn in the Future? Ecological Modelling 115 (1999), pp. 129-148.
  22. Adam Łomnicki, Individual-Based Models and the Individual-Based Approach to Population Ecology, Ecological Modelling 115 (1999), pp. 191-198.
  23. Volker Grimm, Tomasz Wyszomirski, David Aikman, and Janusz Uchmański, Individual-Based Modelling and Ecological Theory: Synthesis of a Workshop, Ecological Modelling 115 (1999), pp. 275-282.

LINKS

Alife

Conferences and Workshops

Corporations

Research Groups and Institutes

Software

QUOTES

QUESTIONS FOR DISCUSSION

Thursday September 7
Tuesday September 12
Tuesday September 26
Thursday October 5
Tuesday October 10
Tuesday October 17
Tuesday October 24
Thursday October 26
Tuesday October 31
Thursday November 2
Tuesday November 7
Thursday November 9
Tuesday November 14
Tuesday November 28
Thursday November 30