CPSC 445 - Algorithms for Bioinformatics

Algorithms for Bioinformatics (CPSC 445)

news archive:

2006/04/15:
The schedule for the oral final examinations is available here. All examinations are held in Holger's office (ICCS X541). Students must be available at precisely the time shown on the exam schedule and are urged to take any measures necessary to ensure timely arrival at the exam location. Late arrivals or missed exams will be handled strictly according to UBC examination rules. As for any UBC examinations, students need to bring student ID and gouvernment-issued picture ID. Each oral exam will take about 15-20 minutes. The examiner (Holger) may ask questions on any materials covered in the course (i.e., lectures, assignments, quizzes), but a significant part of the exam will be focussed on material previously covered in homework assignments and quizzes. Exam questions may involve moderate amounts of calculation as a means of demonstrating knowledge of algorithms covered in the course.
All assignment and quiz results are now available on WebCT.

2006/04/08:
During the week of 10-14 April, Holger's office hours are as follows:

04/10, mon, 11:30-12:30
04/11, tue, 9:00-10:00
04/13, thu, 16:00-17:00
There are no office hours during the week of 17-21 April.
Two papers on the topics covered in Module 6 are now available in the "Resources" section.

2006/04/03: As announced in class, a first draft of the (randomly generated) schedule for the oral final examinations on 19 and 20 April has been generated and is available here. Anyone who cannot make their assigned slot because of conflicts with other examinations (where 'conflict' is used in the sense defined by UBC examination rules) needs to context Holger and Mohammad via e-mail by Thu, 06/04/06. All exam times are preliminary and are subject to modifications. The schedule will be finalised by 06/04/12 (one week before the first exam date). Further details regarding oral examinations, including location, will be posted on the course web page soon.

2006/03/30: Assignment 5 has been released (see "Assigments" section) and is due Thu, 06/04/06, 9:30 (hand-in at the beginning of class). Please make sure to not staple pages of your handin - use paper clips instead, and mark each sheet with your name and student number.

2006/03/28: As announced today in class, Quiz 4 has been scheduled for the first 10-15min of class on Tue, 06/04/04. It will cover material from Module 5 (RNA and protein structure).

2006/03/20: Please complete this questionnaire and hand it in as soon as possible.

2006/03/16:
Please make sure to complete the reading assignment (see 'Assignments' section) for next Tue.
Assignment 4 has been released (see "Assigments" section) and is due Thu, 06/03/23, 9:30 (hand-in at the beginning of class). Please make sure to not staple pages of your handin - use paper clips instead, and mark each sheet with your name and student number.
As announced on Tue in class, Quiz 3 has been scheduled for the first 10-15min of class on Tue, 06/03/21. It will cover material on gene finding (Module 4).

2006/02/28: Assignment 3 has been released (see "Assigments" section) and is due Tue, 06/03/07, 9:30 (hand-in at the beginning of class). Please make sure to not staple pages of your handin - use paper clips instead, and mark each sheet with your name and student number.

2006/02/23:
Please make sure to complete the reading assignment (see 'Assignments' section) for next Tue.
As announced today in class, Quiz 2 has been scheduled for the first 10-15min of class on Thu, 03/02. It will cover material on phylogenetic tree inference (Module 3).

2006/02/09: Assignment 2 has been released (see "Assigments" section) and is due Tue after Reading Week, 06/02/21, 9:30 (hand-in at the beginning of class). Please make sure to not staple pages of your handin - use paper clips instead, and mark each sheet with your name and student number.

2006/02/02:
As announced today in class, Quiz 1 has been scheduled for the first 10-15min of class on Thu, 02/09. It will cover some aspects of pairwise sequence alignment (Module 2).
A link to the pairwise sequence alignment applet used in class has now been added to the "Resources" section. Please note that this applet has a few (relatively minor) bugs.

2006/01/30:
As mentioned in class, information about the bioinformatics reading group can be found here. There is a reading group meeting today (Mon, 06/01/30) at 15:00 in Room X530.
Assignment 1 has been released (see "Assigments" section) and is due next Tue, 06/01/31, 9:30 (hand-in at the beginning of class). Please make sure to not staple pages of your handin - use paper clips instead, and mark each sheet with your name and student number.

2006/01/24:
Assignment 1 has been released (see "Assigments" section) and is due next Tue, 06/01/31, 9:30 (hand-in at the beginning of class).
Links to the animations used today in class have now been added to the "Resources" section.

2006/01/17:
Reminder: As announced last Thursday, Quiz 0 has been scheduled for the first 15min of class on Thu, 01/19. It will cover some aspects of the biological foundations covered so far in Module 1.
Links to the animations used in class have now been added to the "Resources" section.

2006/01/10: The assigned reading for Thu, 06/01/12 (Hofstadter chapter, see "Assignment" section of the course web page) is now available in the ICICS Reading Room.

2006/01/05: Please complete this questionnaire before the first class.

2005/12/27: Due to an emergency in Holger's family, classes on 01/03 and 01/05 have to be cancelled. The first class is on Tuesday, 01/10. Please check the course web page on 01/08 for additional information.

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2006/04/15:		The schedule for the oral final examinations is available here. All examinations are held in Holger's office (ICCS X541). Students must be available at precisely the time shown on the exam schedule and are urged to take any measures necessary to ensure timely arrival at the exam location. Late arrivals or missed exams will be handled strictly according to UBC examination rules. As for any UBC examinations, students need to bring student ID and gouvernment-issued picture ID. Each oral exam will take about 15-20 minutes. The examiner (Holger) may ask questions on any materials covered in the course (i.e., lectures, assignments, quizzes), but a significant part of the exam will be focussed on material previously covered in homework assignments and quizzes. Exam questions may involve moderate amounts of calculation as a means of demonstrating knowledge of algorithms covered in the course. All assignment and quiz results are now available on WebCT.
2006/04/08:		During the week of 10-14 April, Holger's office hours are as follows: 04/10, mon, 11:30-12:30 04/11, tue, 9:00-10:00 04/13, thu, 16:00-17:00 There are no office hours during the week of 17-21 April. Two papers on the topics covered in Module 6 are now available in the "Resources" section.
2006/04/03:		As announced in class, a first draft of the (randomly generated) schedule for the oral final examinations on 19 and 20 April has been generated and is available here. Anyone who cannot make their assigned slot because of conflicts with other examinations (where 'conflict' is used in the sense defined by UBC examination rules) needs to context Holger and Mohammad via e-mail by Thu, 06/04/06. All exam times are preliminary and are subject to modifications. The schedule will be finalised by 06/04/12 (one week before the first exam date). Further details regarding oral examinations, including location, will be posted on the course web page soon.
2006/03/30:		Assignment 5 has been released (see "Assigments" section) and is due Thu, 06/04/06, 9:30 (hand-in at the beginning of class). Please make sure to not staple pages of your handin - use paper clips instead, and mark each sheet with your name and student number.
2006/03/28:		As announced today in class, Quiz 4 has been scheduled for the first 10-15min of class on Tue, 06/04/04. It will cover material from Module 5 (RNA and protein structure).
2006/03/20:		Please complete this questionnaire and hand it in as soon as possible.
2006/03/16:		Please make sure to complete the reading assignment (see 'Assignments' section) for next Tue. Assignment 4 has been released (see "Assigments" section) and is due Thu, 06/03/23, 9:30 (hand-in at the beginning of class). Please make sure to not staple pages of your handin - use paper clips instead, and mark each sheet with your name and student number. As announced on Tue in class, Quiz 3 has been scheduled for the first 10-15min of class on Tue, 06/03/21. It will cover material on gene finding (Module 4).
2006/02/28:		Assignment 3 has been released (see "Assigments" section) and is due Tue, 06/03/07, 9:30 (hand-in at the beginning of class). Please make sure to not staple pages of your handin - use paper clips instead, and mark each sheet with your name and student number.
2006/02/23:		Please make sure to complete the reading assignment (see 'Assignments' section) for next Tue. As announced today in class, Quiz 2 has been scheduled for the first 10-15min of class on Thu, 03/02. It will cover material on phylogenetic tree inference (Module 3).
2006/02/09:		Assignment 2 has been released (see "Assigments" section) and is due Tue after Reading Week, 06/02/21, 9:30 (hand-in at the beginning of class). Please make sure to not staple pages of your handin - use paper clips instead, and mark each sheet with your name and student number.
2006/02/02:		As announced today in class, Quiz 1 has been scheduled for the first 10-15min of class on Thu, 02/09. It will cover some aspects of pairwise sequence alignment (Module 2). A link to the pairwise sequence alignment applet used in class has now been added to the "Resources" section. Please note that this applet has a few (relatively minor) bugs.
2006/01/30:		As mentioned in class, information about the bioinformatics reading group can be found here. There is a reading group meeting today (Mon, 06/01/30) at 15:00 in Room X530. Assignment 1 has been released (see "Assigments" section) and is due next Tue, 06/01/31, 9:30 (hand-in at the beginning of class). Please make sure to not staple pages of your handin - use paper clips instead, and mark each sheet with your name and student number.
2006/01/24:		Assignment 1 has been released (see "Assigments" section) and is due next Tue, 06/01/31, 9:30 (hand-in at the beginning of class). Links to the animations used today in class have now been added to the "Resources" section.
2006/01/17:		Reminder: As announced last Thursday, Quiz 0 has been scheduled for the first 15min of class on Thu, 01/19. It will cover some aspects of the biological foundations covered so far in Module 1. Links to the animations used in class have now been added to the "Resources" section.
2006/01/10:		The assigned reading for Thu, 06/01/12 (Hofstadter chapter, see "Assignment" section of the course web page) is now available in the ICICS Reading Room.
2006/01/05:		Please complete this questionnaire before the first class.
2005/12/27:		Due to an emergency in Holger's family, classes on 01/03 and 01/05 have to be cancelled. The first class is on Tuesday, 01/10. Please check the course web page on 01/08 for additional information.