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CS 297 - Advanced Bioinformatics for Genomics and Transcriptomics

Announcements

  • **NEW** June 06, 2016 -  Here is the final class standing, which is the basis of the grade I will be submitting tomorrow. Should you have any questions regarding the tally, feel free to e-mail me. Also, don't forget to answer the survey which I sent you via email. It has been a blast having you guys for the pilot offering. I really hope you learned something useful from this class. See you around! :)
  • May 31, 2016 -  Here is the final tally for your Machine Exercises and here is the pre-group project class standing.
  • May 23, 2016 - Guidelines for the Written Report now up. See right hand side, last table row. "Deadline" is on June 3, 2016, 11:59pm (see why deadline is in double quotes in Guidelines).
  • May 12, 2016 -  Guidelines for the oral reports and report schedule now up. See right hand side under "Group Project Presentation". See you on May 23!
  • April 12, 2016 - Machine Exercise 3 specs up. See right hand side of the site for the link. Read the instructions carefully. Deadline is on April 22, 2016, 11:59pm.
  • March 31, 2016 - Machine Problem 1 specs up. See right hand side for the download link. Deadline is on April 19, 2016, 11:59pm
  • March 15, 2016 - Machine Exercise 2 specs up. See right hand side of the site for the link. Read the instructions carefully. Deadline is on March 28, 2016, 11:59pm.
  • February 28, 2016 - There is a minor revision to the schedule of activities for the class in view of the cancellation of classes last week. We will be discussing Sequence Alignment tomorrow, February 29, then we will conduct the Machine Exercises for the topic during the first part of the March 7 schedule.
  • February 21, 2016 - NO CLASSES TOMORROW (FEBRUARY 22, 2016)I have to attend to a pressing matter tomorrow. I will be posting an announcement within the week as to changes in the schedule of activities due to this development. Hoping for your patience and understanding.
  • February 1, 2016 - In view of the large time gap before we meet again, here's something to keep you (theoretically) busy over the long "break". This will not be recorded but you can submit your answers to check if you have some significant understanding of the two lessons we discussed so far. Advanced Gong Xi Fa Cai / Xin Nian Kuai Le and see you in two weeks! :)
  • January 30, 2016 - Here are the groups for the class. Sorry for posting it late. For February 1, we will spend the first half of the session to finish the Programming Concepts of the Computational Foundations, followed by the lecture on the Biological Foundations to be conducted by a guest lecturer (TBD). See you by then! :)
  • January 19, 2016 - We need to change venue for our classes due to a conflict in room usage (the other class in conflict has precedence over ours). At least for the next couple of sessions, we'll hold lectures at the ERDT Room. I'll keep you posted on where we will be holding the lab activities once a siginificant development comes up. Really sorry for the inconvenience, and am hoping for your understanding and patience.
  • January 18, 2016 - This is the website for the CS 297 (Advanced Bioinformatics for Genomics and Transcriptomics) class facilitated by Jan Michael Yap. Announcements and files pertinent to the class will be posted here.

DatesLesson Materials
01/18/2016Introduction to the Course
01/25/2016
02/01/2016
Computational Foundations

02/01/2016
Biological Foundations
 02/15/2016 
 Algorithmics and Data Structures
02/29/2016
03/07/2016
Sequence AlignmentClustalX:
Download
Tutorial
03/07/2016
03/14/2016
Phylogenetics and DNA BarcodingMachine Exercise Specs

Phylip:

Download
Tutorial
03/31/2016
04/19/2016
MACHINE PROBLEM 1 Specifications 
03/28/2016
04/04/2016
Genome Assembly
04/11/2016Annotation
ME 3 Specs
Excel template
Datasets:
FL478 down-regulated
FL478 up-regulated
IR29 down-regulated
04/18/2016Variant Calling
04/25/2016
05/02/2016
Association Mapping
R/qtl Tutorials
ME 4 Specs
ME 4 Dataset
05/02/2016
 05/13/2016 
MACHINE PROBLEM 2 Specifications
 05/23/2016 
GROUP PROJECT PRESENTATIONGuidelines
Schedule
06/03/2016WRITTEN REPORT Guidelines 
  • Syllabus can be downloaded here.
  • Copy of the 2012 Code of Student Conduct can be downloaded here.