Reading and Short Programming Assignments for Fall 2012
Assignment 14 (reading, due Tuesday December 4)Read the article by Leloup and Goldbeter and answer these questions.
Assignment 13 (reading, due Thursday November 29)Read the article by Stelling et al and answer these questions.
Assignment 12 (coding, due Tuesday November 20)Finish programing the evolutionary strategy we began in class. The Wikipedia articles on genetic algorithms and evolutionary strategies are also worth reading.
Assignment 11 (reading, due Thursday November 15)Read this article by Locke et al and answer these questions.
Assignment 10 (coding, due Tuesday November 13)Finish coding the three hill-descending methods we discussed in class.
Assignment 9 (coding, due Thursday November 8)I sent an email with the assignment. It is also in this document.
Assignment 8 (coding, due Tuesday October 23)Code up ExplicitTrapezoidal and ExplicitMidpoint. Try to convince yourself these are second order methods by comparing their output to that of ODE15s.
Assignment 7 (coding, due Thursday October 11)Finish the coding we began in class. Reproduce Figures 4A and 4B or 4C and 4D from the paper by Becker-Weimann et al.
Assignment 6 (reading, due Tuesday October 9)Read this article by Becker-Weimann et al and answer these questions. We will write the code for the model in class on Tuesday.
Assignment 5 (reading, due Thursday September 27)Read this article by Mangan and Alon. We will reproduce one of the figures in class on Thursday.
Assignment 4 (reading, due Tuesday September 25)Read the hand-out from class (skipping section 2.4.1). Answer these questions.
Assignment 3 (reading and coding, due Tuesday September 18) and its paper
Assignment 1 (reading, due Tuesday September 11)The reading assignment involves a list of questions to answer about the articles and chapter section listed below. I suggest you read the questions before embarking on your article-reading adventure. The questions indicate what I consider to be the most relevant points made in the articles. When answering the questions, you may be as high- or low-tech as you wish, but please turn in your reponses via email or in person by the beginning of class on Friday.
- The Universal Features of Cells on Earth -- a section in Ch. 1 of Molecular Biology of the Cell, ed. B Alberts, 4/e, 2002 (note: there is a new edition of the book, but this is the one freely available on the web)
- Systems Biology: A Brief Overview by H Kitano, Science, 2002. (PDF on Moodle)
- Computational systems biology by H Kitano, Nature, 2002. (PDF on Moodle)
- Can a biologist fix a radio: or what I learned while studying apoptosis by Yuri Lazebnik, Cancer Cell, 2002. (PDF on Moodle)