CSE P590A,  Su '06:  Assignment #1, Due: 6/29/06

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1. Required Reading: Read "Molecular Biology for Computer Scientists" by Hunter, linked from the course home page. (If you already happen to have a good background in molecular biology, contact me; we can arrange a useful substitute.)

2. Post a note about it on the class message board. (See course FAQ for general info on our expectations for and grading of these posts, which we'll be doing most weeks.) In your note, tell us at least the following: (a) one thing you found particularly surprising, (b) one thing that you are curious to learn more about and (c) one statement of "fact" that you think has since been proven to be false (the paper is over 10 years old; most of it is rock solid, but not all).

3. Free reading: Find and read additional materials on some topic that you feel amplifies what you learned from Hunter, goes deeper into one of the topics, covers extra stuff, corrects Hunter's occasional errors based on more modern data, etc. Can be one or more articles, technical papers, web pages, book chapters or whatever, totaling 30+ pages. Anything from The Cartoon Guide to Genetics to Nobel prize-winning work is fair game.

4. Post links and/or citations to what you read, together with a few sentences about it/them. E.g., give me a critique of it for meeting your needs. Who would it have been good for, if not you? Highlight something from it that you found especially interesting or surprising. If you have read the same article as someone who previously posted, it's fine to agree/disagree with their assessment of the article, but say why, not just "me too".

5. Extra Credit: The technical vocabulary in bio papers is dense and daunting to CS students. Websters and Wikipedia can help, but there are doubtless better sites with glossaries and short, gentle introductions to these concepts that don't suffer too much from, e.g., the curse of recusive jargon. If you find one you like, post a link and a sentence or two about it.

6. After you finish the weekly homework, please respond to this simple, one-question Anonymous Poll

Your free reading may come from anywhere (online or not). The following random starter suggestions are gleaned from multiple sources, including past student recommendations, and I have not even clicked all the links, let alone read them all, so follow your own instincts as to whether they will be useful to you.

• A Quick Introduction to Elements of Biology, a primer by Alvis Brazma et al.
• S-Star Bioinformatics Online Course Schedule, a collection of video primers
• One student reports that bioinformatics.org has "a very comprehensive FAQ which included several references to online tutorials and lectures. The FAQ itself could serve as a good annotated reference list."
• The "Online Courses" pages at iscb.org may also be useful.
• CSE 490C: Computational Biology .
• CSE 590TV: Computational Biology (Professional Masters Program, 2003) .
• CSE 527: Computational Biology .
• CSE 590C: Reading & Research in Computational Biology .

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