CAP 5510 & CGS 5166: Spring 2008
Bioinformatics Course Homepage
Tue & Thu 11:00 - 12:15, ECS 132

• Apr 22: Important: Final Exam may be started at any time after 4:30 PM today. You will return the exam by 5PM on Thursday, April 24, or 24 hours after it was maield to you, whichever is earlier. This rule is strict and there will be no exceptions. Failure to return the exam on time will result in a fail grade for the class. Email me with the time when you would like the exam to be mailed to you.
  You may turn in your final project report by 5PM this Friday.
• Apr 19: This evening we are having a pot-luck dinner party at my house. You are all invited. Check your email for details on time and directions. A quick response to my email would be appreciated, regardless of whether you are able to come or not.
• Apr 14: Homework #2 has been graded. Pick it up at your convenience.
• Apr 8: Homework #1 has been graded. Pick it up at your convenience.
• Apr 8: Project presentation schedules:
  April 17: 1) Anna Shen (10:00AM), 2) Deepak Balasubramanian (10:30 AM), 3) Yi Zhang (11:00 AM), 4) Allison Lanager (11:30 AM);
  April 22: 5) Diansy Zincke (10:00AM), 6) Varinder Pannu (10:30 AM), 7) Sean Leslie (11:00 AM), 8) Brian Kunkle (11:30 AM).
• Apr 2: We have finished covering the syllabus in class. We will meet once again on Tuesday, April 8 at 11:00 AM, to discuss expectations on the project, the final report, the final exam, and course evaluation. After that, we will meet again for your presentations (April 15 and 17).
• Apr 1: For those of you planning to finish an entire semester project in the remaining one week, let me remind you that it represents 50% of your grade.
• Mar 30: Schedule for Project:
  Final Report Due: Fri, April 11, 2008; 12 days away!
  25-min Presentations: Tue and Thu, April 15 and 17, 2008 (Attendance Mandatory!)
• Mar 30: Final Exam: 24-hour Take Home exam on April 23/24
  
• Mar 19: Your classmates found some minor typos in Homework 2. A modified version is now available below.
• Feb 26: Today we will have class starting from 10:05 AM
• Feb 20: Tomorrow we will have class starting from 10:05 AM
• Feb 18: Tomorrow we will have class starting from 10:05 AM
• Feb 11: Tomorrow we will have class starting from 9:30 AM through 12:15 PM with a 15 minute break in between. Please be in on time.
• Feb 05: Homework 1 is now ready. See below.
• Jan 29: If you are interested in research in this area, please visit the website for the Bioinformatics Research Group @ FIU.

• For CS Majors: CAP 5510
• For NON-CS Students: CGS 5166

• Bioinformatics, by David Mount, CSHL Press, 2002, 2nd Edition, Paperback, ISBN: 0-879-69712-1
• Bioinformatics, by Baxevanis & Ouelette, 3rd Edition, ISBN: 0-471-47878-4.
• [REFERENCE] Understanding Bioinformatics, by Zvelebil & Baum, ISBN: 0-815-34024-9.

• Homework 1 (Due Feb 19, 2008);
• Homework 2 (Due Mar 13, 2008); [New Due Date: Mar 20, 2006];
  Your classmates found some typos in the homework. I have corrected some of these errors and a modified version is now available from Modified Homework 2.

• Jan 22: Lec 1[pdf] [Introduction & Motivation]; Reading: [Chapters 1, 2 (from DM); Extra]
• Jan 24: Lec 2[pdf] [Motivation & Biological Preliminaries]; Reading: [Same as Above]
• Jan 29: Lec 3[pdf] [Sequence Alignment & BLAST]; Reading: [Chapter 11 (from BO); Chapter 3 (from DM); Extra]
• Jan 31: Lec 4[pdf] [Sequence Alignment & BLAST]; [Chapter 12.1-12.4 (from BO); Chapter 6 (from DM)]
• Feb 05: Lec 5[pdf] [Suffix Trees; Multiple Sequence Alignments]; [Chapter 4 (from DM) for Statistics of alignments; Chapter 5 (from DM) until page 189]
• Feb 07: Lec 6[pdf]
• Feb 12: Lec 7[pdf]
• Feb 14: Lec 8[pdf]
• Feb 19: Lec 9[pdf]
• Feb 21: Lec 10[pdf]
• Feb 26: Lec 11[pdf]
• Feb 28: Lec 12[pdf]
• Mar 03: Lec 13[pdf]
• Mar 05: Lec 14[pdf]
• Mar 11: Lec 15[pdf]
• Mar 25: Lec 16[pdf]
• Mar 27: Lec 17[pdf]
• Apr 1: Lec 18[pdf]

• Popular [Posted Jan 9]: California Sea urchin genome sequenced, Nov 2006.
• Popular [Posted Feb 4]: Time, Love, Memory, by Jonathan Weiner, 1999.