Paul Grobstein, Bryn Mawr College Department of Biology
Clare Congdon, Bryn Mawr College Computer Science Program

Schedule of Topics and Assignments

Each week, students will have outside readings and projects to work on, and report on their progress in these to their on-line web journals (in addition to discussing them during class time).

Go straight to a specific week:
January 22, January 29,
February 5, February 12, February 19, February 26,
March 5, (March 12), March 19, March 26,
April 2, April 9, April 16, April 23, April 30,

January 22:	Introduction
	In Class: Introduction to complex systems How to run StarLogo How to keep web journals Introduction to Unix Reading for Next Week: Sigmund, chapters 1 and 3 Project for Next Week: Lab 1: Running StarLogo program, and reporting back to class (and journal) what you observed CS students: start learning Unix/Emacs/Java Bio students: start learning Unix/TextEdit/HTML All students: start thinking about Project 1, due March 5
January 29:	Linear vs. Non-Linear
	In Class: Discuss projects from previous week Linear vs. non-linear Introduce "On Beyond Newton" A little Unix, a little HTML, a little Java Reading for Next Week: Sigmund, chapter 2 Read about Java, such as: Java Documentation from Sun , "What is Java" link, primarily the few paragraphs subtitled "So what exactly is Java?"; the history and egos are for your amusement. Project for Next Week: Lab 2: Experimenting with On Beyond Newton and reporting back to class (and journal) what you observed All students: more Unix/Emacs/Java Set personal computer-skills goals and pursue them.
February 5:	Game of Life and Cellular Automata
	In Class: Discuss projects from previous week Cellular Automata in general and Game of Life in particular A little Unix, a little HTML, a little Java Reading for Next Week: Sigmund, Chapter 4 Project for Next Week: Lab 3: Experimenting with Life/CA's and reporting back to class (and journal) what you observed All students: start thinking about Project 1, due March 5
February 12:	Randomness
	In Class: Discuss readings and projects from previous week A little Unix, a little HTML, a little Java Reading for Next Week: Resnick - the first two chapters and enough of the third to get a feeling for the development of and command structure for particular models Project for Next Week: Lab 4: Randomness All students: submit outline for Project 1, due March 5
February 19:	StarLogo
	In Class: Discuss readings and projects from previous week A little Unix, a little HTML, a little Java Reading for Next Week: Resnick -- finish Braitenberg, Chapters 1-4 Project for Next Week: All students: work on project due March 5; report to journal on your progress
February 26:	Catchup
	In Class: Discuss Resnick and Braitenberg Discuss progress and problems with projects Help with individual problems Reading for Next Week: (nothing; work on project) Project for Next Week: All students: work on project due March 5; report to journal on your progress
March 5:	Class presentations on Project 1
	In Class: Presentations on Project 1 Reading for After Break: Finish Braitenberg Project for After Break: (nothing -- extension on finishing Project 1)
March 12:	(Spring Break)
March 19:	Neural Nets: Complex, Distributed Information Processing Systems
	In Class: Discuss Braitenberg reading (rest of book) Introduction to Neural Nets Reading for Next Week: Neural Networks and the Computational Brain, from the Brain Project, by Stephen Jones The Appeal of Parallel Distributed Processing - Chapter 1 of Parallel Distributed Processing, by J.L. McClelland, D.E. Rummelhart, and G.E. Hinton Naturally Intelligent Systems, Chapters 1-3, by M. Caudill and C. Butler Project for Next Week: Lab 6: Understanding and building neural nets
March 26:	Neural nets: Learning, Generalizing ... Evolving?
	In Class: Backpropagation Reading for Next Week: Plunket and Ellman Project for Next Week: Lab 7: Backpropagation: using neural nets to find solutions
April 2:	Adaptive Systems (Genetic Algorithms)
	In Class: Introduction to Genetic Algorithms Reading for Next Week: Scientific American, July 1992, Holland and Riolo (optional: Chapter 9, Mitchell) Chapter 1, Holland, Hidden Order start reading Chapter 2, Holland, Hidden Order Project for Next Week: Lab 8: Genetic Algorithms
April 9:	Adaptive Systems (Tierra or GP)
	In Class: Reading for Next Week: Project for Next Week: Lab 9: Genetic Programming
April 16:	Adaptive Systems
	In Class: Reading for Next Week: Project for Next Week: Lab 10:
April 23:	Catch-up
	In Class: Reading for Next Week: Project for Next Week: (none; work on projects
April 30:	Final Project Presentations

Biology Computer Science Bryn Mawr College

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