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CMPUT 606: Optimization in Bioinformatics (Winter 2025)
eClass: https://canvas.ualberta.ca/courses/18442
Overview:
An introduction to the classic and current research in Bioinformatics and Computational Biology
allowing you to get some hands-on experience by working on a course project.
We will introduce various formulated optimization problems and you will find various computing techniques applicable.
Course Objectives:
- Learn some classic and currently hot research topics in bioinformatics and computational biology;
- learn computing techniques for this area of research;
- be familiar enough to explain these topics to others and understand what contributions you could make.
Student Academic Integrity Policy
Student Conduct Policy
Department Course Policies
| Time |
Monday |
Tuesday |
Wednesday |
Thursday |
Friday |
| noon |
|
| 1:00pm |
|
| 2:00pm |
|
Possible project meetings
(by appt) |
|
|
Lecture B1 (GSB 8-11) |
| 3:00pm |
Possible project meetings
(by appt) |
|
| 4:00pm |
|
Recording of teaching is permitted only with the prior written consent of the instructor or if recording is part of an approved accommodation plan.
Recommended readings (no required textbook):
- L. Gonick and M. Wheelis (1991). "The Cartoon Guide to Genetics". Harper Perennial.
- A. M. Lesk (2002). "Introduction to Bioinformatics". Oxford Univ. Press.
- D. Gusfield (1997). "Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology". Cambridge Univ. Press.
- P. Baldi and S. Brunak (2001). "Bioinformatics, the Machine Learning Approach". The MIT Press.
- T. H. Cormen, C. E. Leiserson, R. L. Rivest, and C. Stein (2009).
"Introduction to Algorithms (Third Edition)". The MIT Press.
Lecture Schedule:
| Week |
Date |
Lecture Topics |
| 1
| Jan 10
| Course overview;
discussion on how to run the course (below is one version);
biology background introduction
|
| 2
| Jan 17
| Sequencing
|
| 3
| Jan 24
| Sequence and string comparison
Exercise #1 (10%) on sequencing due 26th
|
| 4
| Jan 31
| Phylogenetic analysis
Exercise #2 (10%) on sequence comparison due 2nd
|
| 5
| Feb 7
| Genotyping and genome-wide association study
Exercise #3 (10%) on phylogenetic analysis due 9th
|
| 6
| Feb 14
| Gene expression and data analysis
Exercise #4 (10%) on genotyping/halpotyping due 16th
|
| 7
| Feb 21
| Family Day, Reading Week
|
| 8
| Feb 28
| Missing data imputation
Exercise #5 (10%) on clustering, classification, regression due 2nd
|
| 9
| Mar 7
| Student project proposal presentations
- 2:10pm (see Google Drive)
- 2:40pm
- 3:10pm
- 3:40pm
- 4:10pm
|
| 10
| Mar 14
| Student project proposal presentations
- 2:10pm (see Google Drive)
- 2:40pm
- 3:10pm
- 3:40pm
- 4:10pm
Course project review, proposal due 16th
|
| 11
| Mar 21
| Protein properties
|
| 12
| Mar 28
| Protein structure comparison, determination, and prediction
|
| 13
| Apr 4
| Proteomics and metabolomics
Course project final report due 9th
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Grading Scheme:
- Check my marks
- There is no exam.
- Mark distribution:
- 50% 5 weekly programming exercises and numerical experiments (10% each);
- 20% course project proposal + presentation (background, existing work, methods, expected results, rationale);
- 30% course project final report (literature review excluded).
- Notes:
Each student to create a GoogleDrive (w/sub-directories) containing all your work to share with your instructor;
New: eClass has been created and please try to make submissions there;
- a `readme` file (or `makefile`) to run your program and replicate your results.
(Failing to replicate your results is automatically a zero.)
- A presentation is worth half of the marks;
- One can choose to present their project during Weeks 11-13, if highly aligning with lecture topics.
Disclaimer: Any typographical errors in this Course Outline are subject to change and will be announced in class.
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