General information and office hours (Spring 2013):
- course time and location: Tuesdays and Thursdays 14 - 15.30 h in room DMP 101 of the DMP building
- office hours:
- Mondays: 14-16 h X551 (Irmtraud Meyer)
- Fridays: 11-12 h X551 (Irmtraud Meyer)
- Note: all office hours are on the 5-th floor of the ICICS/CS building
Important dates (Spring 2013):
- January 3: course starts
- January 14: last day of withdrawal from course without "W" mark
- January 24 (Thursday): deadline for submitting your course project proposal
- February 8: last day of withdrawal from course with "W" mark
- February 18-22: term break (no classes and office hours)
- February 26 (Tuesday): deadline for submitting your interim course project report
- April 4: last class
- April 11 (Thursday), 12 h (noon): deadline for submitting your final course project
Course syllabus:
Goals of the course:
The purpose of this advanced course in Bioinformatics is to introduce you the
algorithms and probabilistic methods that are currently being used to capture and analyze
the complexities of today's biological data. The aim of the course is to bring
you to a level of expertise which should allow you to embark on your own
research projects in Bioinformatics and to let you explore one research area in more depth
through a course project.
Format of the course:
This graduate course is meant to prepare you for research in Bioinformatics. This involves
learning how to critically present and discuss published research and how to prepare
and conduct a small research project of your own. CPSC 545 has the format of a reading group
where the students present and discuss original papers as well as the relevant technical and
biological background. Each student is required to:
- prepare the reading material for all meetings and actively
participate in all and lead some discussions (see here for details),
- give one or more presentations and
- complete a course project.
Registering for the course:
Please do not email me, but first check the departmental web-pages if you require more information on how to register
for this course or email Joyce Poon (poon [at] cs.ubc.ca), our graduate program administrator.
Prerequisites:
CPSC 545 is aimed at students who have already successfully completed CPSC 445 or an equivalent
course at a different university. In order to benefit from this course, you
- have to have successfully completed a course on algorithms for Bioinformatics
comparable to UBC's CPSC
445 (if in doubt, check
the learning goals
of CPSC 445 and contact me),
- have a strong motivation to learn more about active areas of research in Bioinformatics,
- have already been exposed to some algorithms through other courses,
- be confident programming in either Java or C++ and
- be familiar with basic probability theory and know the basics of biology.
I understand that different graduate students will come with a slightly
different background knowledge and am happy to cater for a diverse audience by
providing pointers to the literature throughout the course. However, as this is graduate
level course, I expect the student to take the initiative in making sure s/he catches up with
whatever knowledge or skill s/he is lacking.
Reference books:
- the book "Biological sequence analysis" by Durbin et al. (Cambridge University
Press, ISBN-13: 978-0521629713) will serve as our main reference book (the BSA book)
- if you do not have a strong Biology background, I suggest "Molecular Biology of
the Gene" by James Watson et al. (Benjamin Cummings, 6th edition (2007), ISBN-13 978-0805395921) and, to a
lesser extent, "Molecular Biology of the Cell" by Bruce Alberts which is also a fine book (Garland, 4th edition
(2002), ISBN-13: 978-0815332183) as your reference books. Make sure you are dealing with the latest editions
of these books.
Grading:
Course grades will be determined based upon the following (with approximately equal weight):
- Class participation. Each student is required to prepare all the assigned reading material
for all classes and participate actively in the material's discussion. You
also need to be prepared to lead one or more discussions.
Your class participation will be judged by the quality and
quantity of the contributions that you make during all classes, see
here for details.
- Class presentations. Each student is required to give one or more class presentations.
The presentation should cover the assigned material in the specified time, see
here for details.
- Course project. Each student is required to complete a course project. The course
project either involves a review paper or a programming project, see here
for details. In the interest of fairness to all students, the deadline for
submitting the course project will be strictly inforced. Late submissions
incur a penalty of 25% per day, i.e. 75% is the maximum you can obtain if
you submit within the first 24 hours after the
deadline, 50% the maximum within the first 48 hours after the deadline etc.
Auditing CPSC 545 requires active participation in all classes and successful
class presentations, but no course project.
If you happen to be ill:
As class participation amounts to a third of your final mark, you need to
- email me as early as possible if you cannot attend a class to due illness and be prepared to provide a doctor's notice for the day(s) in question, especially
if this concerns the day of your presentation.
- also contact your teaching buddy as early as possible (this is the person doing the last presentation before yours) and
hand over your presentation material so s/he can give your presentation, in case you happen to be ill on the day of your presentation.
Please ensure you check the overview of university guidelines and help pages.
Important notes on plagiarism:
Submitting the work or ideas of another person as your own (i.e. plagiarism) constitutes
academic misconduct. Please make sure you are aware of the following UBC documents:
Violations of these rules constitute very serious academic misconduct, and they are
subject to penalties ranging from a grade of zero on a particular assignment to
indefinite suspension from the University. More information on procedures and
penalties can be found in the Department's Policy on Plagiarism and collaboration and
in the University Calendar. If you are in any doubt about the interpretation of any of
these rules, consult your instructor.
Updated: January 2013, Irmtraud Meyer
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