Q'BIC Capstone Workshop 2009
Bioinformatics Component

• Jul 03: Homework #2 is ready. See below.
• Jul 01: Here is what we decided today:
  (a) You need to email me by end of today on the topic you choose for the project for this class.
  (b) Your project presentation will be on Tuesday, July 7, in class.
  (c) Each presentation will be for 15 minutes (12 minutes presentation + 3 minutes questions). You can break down the presentation into 3-4 min background, 3-4 technical stuff, and 3-4 min experiments, results, and conclusions. There will be peer evaluation of your presentation;
  (d) You need to write a paper on your project. This will be due on Thursday, July 9, in my office. It should be a minimum of 3 pages long (maximum upto 10 pages) in 12pt font, single-spaced (exclusing figures and references).
  (e) The paper should describe the introduction/motivation of the work, the technical aspects, bioinformatic analysis and tools that may be relevant, results and conclusions.
  (f) There will be no final exam for this section of the course.
  
• Jun 30: Email me the topic of your choice and your team member as soon as possible. Your 2nd homework will be ready this Friday. It will be due on the following Tuesday.
  
• Jun 29: List of projects for the term paper is ready. See below.
• Jun 26: Homework #1 is ready. See below. Expectations and rules for the paper will be discussed in class.

• Summer Workshop

• Bioinformatics and Functional Genomics, by Jonathan Pevsner, Wiley-Blackwell, Paperback, 2nd Edition, ISBN 978-0-470-08585-1
• [REFERENCE] Bioinformatics, by David Mount, CSHL Press, 2002, 2nd Edition, Paperback, ISBN: 0-879-69712-1
• [REFERENCE] Bioinformatics, by Baxevanis & Ouelette, 3rd Edition, ISBN: 0-471-47878-4.
• [REFERENCE] Understanding Bioinformatics, by Zvelebil & Baum, ISBN: 0-815-34024-9.

• Homework 1: Click here: Due Jun 30, 2009.
• TERM PAPER: List of projects -- Click here: Due Jul 7, 2009; Also, find all 16 papers mentioned in the Projects list: Click here.
• Homework 2: Click here: Due Jul 07, 2009. No Extensions are possible this time!

• Jun 24: Lec 1[pdf] [Introduction & Motivation]; Reading: [Chapters 1, 2 (from JP); Extra]
• Jun 25: Lec 2[pdf] [Biological Preliminaries; Sequence Alignment]; Reading: [Chapters 2, 3, 4 (from JP); Extra]
• Jun 29: Lec 3[pdf] [Sequence Alignment & BLAST]; Reading: Extra
• Jun 30: Lec 4[pdf] [Hidden Markov Models]
• Jul 01: Lec 5[pdf] [Gene Expression; Microarrays]
• Jul 02: Lec 6[pdf] [Next Generation Sequencing]

• Popular California Sea urchin genome sequenced, Nov 2006.
• Popular Time, Love, Memory, by Jonathan Weiner, 1999.