Classes:
Tue+Thu, 9:30-11:00
in DMP 301
First class: Tue, 2006/01/08
Instructor:
Holger H. Hoos
E-mail: hoos "at" cs.ubc.ca
Teaching Assistant:
Final Exams:
Oral exams will take place on the Monday the 21th and Tuesday the 22st of April, 2008
in room X541 (Holger's office). Oral exams will be around 15 minutes long, and a 5 minute
extension is allowed if the instructor deems it necessary. If you cannot attend your given
time slot, contact Holger immediately.
We strongly encourage you to arrive 15 minutes prior to your exam start time, and plan
your trip to campus carefully. You are responsible for arriving to your exam on time.
Because of the tight schedule, we won't be able to accommodate any reschedule delays.
The exams schedule is as follows:
Andrew Carbonetto (acarbo "at" cs.ubc.ca)
New office hours for week of April 14th:
Wed, 14:00-16:00 (ICICS/CS X530)
| April 21th | ||
|---|---|---|
| start time | end time | student |
| 8:30 | 8:50 | Paul Lu |
| 8:50 | 9:10 | Tracy Wilkinson |
| 9:10 | 9:30 | Adam Tarnowsky |
| break | ||
| 9:45 | 10:05 | Bryan Holland |
| 10:05 | 10:25 | Varun Ramraj |
| 10:25 | 10:45 | Michael Chuang |
| break | ||
| 11:00 | 11:20 | Lina Hu |
| 11:20 | 11:40 | Wang Yip |
| 11:40 | 12:00 | Nicholas Wiebe |
| lunch | ||
| 13:00 | 13:20 | Bill Wu |
| 13:20 | 13:40 | Adrian Cortes |
| 13:40 | 14:00 | Kaida Ning |
| break | ||
| 14:15 | 14:35 | John Cheu |
| 14:35 | 14:55 | Qin Zheng |
| 14:55 | 15:15 | Carla Reyes |
| break | ||
| 15:30 | 15:50 | Raymond Lim |
| 15:50 | 16:10 | Mark Sun |
| 16:10 | 16:30 | Lewis Zhou |
| April 22th | ||
|---|---|---|
| start time | end time | student |
| 8:30 | 8:50 | Keane Lim |
| 8:50 | 9:10 | Ernest Tsang |
| 9:10 | 9:30 | Ben Vander Valk |
| break | ||
| 9:45 | 10:05 | Michael Joya |
| 10:05 | 10:25 | Cheyenne Kamran |
| 10:25 | 10:45 | Wendy Leung |
| break | ||
| 11:00 | 11:20 | Tracy Mew |
| 11:20 | 11:40 | King Long Tse |
| 11:40 | 12:00 | Vaneet Lotay |
| lunch | ||
| 13:00 | 13:20 | Jenny Qing Qian |
| 13:20 | 13:40 | Sarah Batara |
| 13:40 | 14:00 | Elena Surkova |
About this course:
Bioinformatics involves the application of computational methods to answer or provide insight on questions in molecular biology. This course provides an introduction to the design and analysis of algorithms for bioinformatics applications. Topics covered will include sequence alignment, phylogenetic tree reconstruction (parsimony and distance-based methods), prediction of RNA and protein structure, gene finding, and motif finding. Algorithmic techniques that will be discussed include dynamic programming and heuristic search methods, as well as combinatorial algorithms for exploration of graphs and trees. Statistical models of molecular sequence and structure, such as hidden Markov models and stochastic context free grammars, and associated algorithms, will also be covered.
Prerequisites:
CPSC 320 and six credits of BIOL beyond BIOL 111, or equivalent. Experience with design and analysis of algorithms is essential for this course. Related texts listed below, such as “Molecular Biology of the Cell”, will be useful for those who need to catch up on biological background. The algorithms texts by Cormen et al. and by Kleinberg and Tardos provide useful background on combinatorial algorithms, including graph algorithms and dynamic programming algorithms. The text by Hoos and Stützle is a more advanced text which provides very useful background on local search techniques.
Recommended Textbook:
Durbin, Eddy, Krogh, Mitchison: Biological Sequence Analysis. Cambridge University Press, 1998
You can access the course wiki here: Course Wiki
These pages are currently viewable by anyone. All members of the course may edit these topic pages and attach shared material. To do so, your CS TWikiName (a registered ID of the form of FirstnameLastname) must be added to the course access list by the instructor or TA.
To get a CS TWikiName:
Students with CS Undergrad Accounts (ex a1a1): register here and then forward the TWikiName you used to Andrew (or Holger). NOTE: when you log in, you'll use your registered email address and password, not your TWikiName.
Students with CS Grad Accounts: your cs login and password gains you some levels of access throughout the CS Twiki, however your TWikiName is how you are granted access to particular protected areas. Register here and forward your TWikiName to Andrew (or Holger).
Once you've been added to the group access list, you should be able to edit as well as view the cs445 web pages.
However, you still need to authenticate yourself for any given session. To trigger the logon dialog, use e.g.
https://bugs.cs.ubc.ca/cgi-bin/twiki/logon/CS445/
rather than https://bugs.cs.ubc.ca/cgi-bin/twiki/view/CS445/
Remember that the login dialog wants your email address (the one you registered if it's non-cs, otherwise your department logon) not your twikiname. Users don't ever have to explictly use their twikinames, which are for internal authentication.
Missed Course Work and Academic Misconduct:
Students will prepare a mini-project on a subject related to the course (computer science and bioinformatics). Students will form a group of 2, and no other sized group will be accepted except under strict circumstances. The mini-projects will include a 1/2 page topic outline, a 10 minute presentation (+ up to 5 minutes of questions), and a 3 page report.
Groups should include 2 references. References should either be a literature paper or similar reputable source (ie not wikipedia). If you are unsure whether a reference is acceptable, please consult either Holger or Andrew. The names and student numbers of both groups members should be included. No two groups may select the same reference or topic. Overlap will be resolved on a "first come, first served" basis.
The topic selected should be related to the course material (see the course outline), a topic from any of the text references (including the course textbook) or a topic pertaining to algorithms in bioinformatics. Topics should be above and beyond the material explained in class. If you unsure whether a topic is acceptable, do not hesitate to contact either Holger or Andrew.
| April 1st, 2008 | ||
|
1. |
Michael Chuang John Cheu | FASTA vs BLAST |
|
2. |
Lingxiao Lewis Zhou Paul Lu | How to Find Optimal Alignments in Linear Space |
|
3. |
Vaneet Lotay Michael Joya | Neighbor Joining Method: A Popular Algorithm for Constructing the Topology of Phylogenetic Trees |
|
4. |
Lina Hu Wang Yip | MSAID: multiple sequence alignment based on a measure of information discrepancy |
|
5. |
Adrian Cortes Ben Vander Valk | Using Sequence Alignment to Discern Germline Gene Fragments of Antibody Sequences |
| April 3rd, 2008 | ||
|
1. |
Jenny Qing Qian Kaida Ning | Algorithms for Short Sequence Assembling |
|
2. |
King Long Tse Qin Zheng | PSI-BLAST |
|
3. |
Elena Surkova Bryan Holland | Protein Secondary Structure Prediction |
|
4. |
Sarah Batara Cheyenne Kamran Keane Lim | The Evolution of Multiple Sequence Alignment Programs |
| April 8th, 2008 | ||
|
1. |
Bill Wu Ernest Tsang | Parital Order Multiple Sequence Alignment |
|
2. |
Varun Ramraj Carla Reyes | Parallel Strategies for Sequence Alignment |
|
3. |
Raymond Lim Nick Wiebe | Prediction of Conserved RNA Secondary Structure within Protein-coding Regions |
|
4. |
Adam Tarnowsky Tracy Wilkinson | Haplotype Inference Algorithms |
|
5. |
Mark Sun Tracy Mew | Local Multiple Sequence Alignment using the Biclustering Technique |
Note: If two groups would like to switch presentation slots, please send an email to Andrew or Holger cc'ing members of both groups.
Reading: