This outline is also available in PDF.
Held: Tuesday, 1 September 2009
We continue our introduction to bioinformatics by exploring a few
of the primary articles on the identification of dinosaur DNA.
- Reading: Chapter 1. Asara et al. 2007. Pevzner et al. 2008. Schweitzer et al. 2009..
- Due: Reading response to Science articles.
- Please fill out the RISC Survey asap.
- For Thursday, do a peer review of two of your colleagues' response papers. (Details to follow in class.)
- We will start the Web exploration in class today and continue it on Thursday. You and your partner(s) should turn in answers to the Web exploration questions next Tuesday.
- Dinosaur DNA, revisited.
- What is bioinformatics?, revisited.
- The joys of interdisciplinarity.
- Web exploration.
Vida will be leading this discussion. These are a few thoughts,
comments, etc., from Sam.
- After reading the primary literature, do you think that the Wired
article was accurate in its description of the science involved?
- What is the process by which the authors used mass spec. to identify
- Is that process novel or well established? How do you know?
- What role does biology play in this process?
- What role does computer science play in this process?
- How much computation is required?
- What are Pevzner's primary criticisms?
- What does the book tell us that bioinformatics is?
- How does that relate to your own perspective on bioinformatics?
- This course is supposedly interdisciplinary. What does that
- Can we be interdisciplinary while preserving the integrity of disciplines?
- Can we be interdisciplinary without deep knowledge of our own field?
- Can we be interdisciplinary without deep knowledge of another field?
- As we suggested on the first day, Sam and Vida will do our best to model
what it means to be a multi-disciplinary team. We both have deep knowledge
of our own fields (or so we hope) and shallow knowledge of each other's
- Will that be enough?
- How will we cope with the incomplete knowledge?
- Rather than using the Web exploration from the book, we will use our
- Create a team of three people which includes at least one person who has
taken some biology and at least one person who has taken some computer
- Your goal is to find out some things about favism using some
extant bioinformatics data resources, primarily at the National Center for