BY659/CS659
FALL 2012
Lecturer: James F. Lynch
Office: SC-381
Telephone: 268–2374
email: jlynch@clarkson.edu
Office hours: MWF 9:15AM–10:00AM,
11:00AM–12:00PM
Lecture hours: MF 8:00AM–9:15AM,
336 Science Center (COSI Lab)
Text: Agent-Based and Individual-Based Modeling: A Practical Introduction, Steven F. Railsback and Volker Grimm, Princeton University Press
(2012), ISBN 978–0–691–13674–5.
GRADING
Grading will be based on homework assignments and
projects. Attendance and participation
in class will also be an important factor in your grade. There will be no exams or final.
READING
ASSIGNMENTS
Monday, September
3
Stefanie’s answer to question 1
Reshica’s answer to
question 1
Astrid’s answer to question 1
Monday, September
17
Friday, September
21
Monday, September
24
Friday, September
28
Friday, October 5
Monday, October 8
Monday, October 15
Friday, October 19
Monday, October
22
Monday, October
29
Friday, November
2
Monday, November
5
Friday, November
9
Monday, November
12
Friday, November
16
Monday, November
19
Monday, November
26
Friday, November
30
Monday, December
3
Friday, December
7
Friday, December
14
LINKS
- Concurrent
biological processes
- Deborah
Gordon: the emergent genius of ant
colonies, video on TED.com
- A
Different Kind of Secret Code - ScienceNOW
- Robots at the Intelligent
Autonomous Systems Laboratory - contains link to Slugbot
- Life on
Earth: Why Biodiversity Varies
- Life-like
cells are made of metal, New Scientist, 14 September 2011
- Modelling E. coli, files from Prof. Vic
Norris’s lecture at Workshop on Systems Biology, Turku, Finland, 2004.
- Paul
Stamets on 6 ways mushrooms can save the world
- Systems
biology for beginners
- Transactions on
Computational Systems Biology
- Tutorial on E.
Coli Chemotaxis; Robustness of the Chemotaxis Circuit, U. Alon
- William L. Romey, SUNY Potsdam, Research in Grouping Behavior
- Roger
Alsing, Genetic Programming: Evolution of Mona
Lisa, weblog
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