CISC-471: Computational Biology

(also known as: CMPE-471)

(Winter 2016)

Last Modified:

PLEASE NOTE: The final exam for the course this winter will take place as follows:
DATE: APRIL 8, 2016
TIME: 2:00 - 5:00
LOCATION: Goodwin HALL room 247 (our classroom)
Education is not the filling of a pail, but the lighting of a fire. Plutarch.

Quick Links

Grading
Homework
Outline and Schedule

Course Instructor

David Rappaport
GOODWIN HALL Room 532
E-MAIL: daver AT cs dot queensu dot ca
OFFICE HOURS: Monday 13:00 - 15:00.

Class Hours

Monday 11:30-12:30 Goodwin 247
Tuesday 13:30-14:30 Goodwin 247
Thursday 12:30-13:30 Goodwin 247

Text

Neil C. Jones and Pavel A. Pevzner (2004) An Introduction to Bioinformatics Algorithms, MIT Press.
I will be following this book and referring to it as the "text". If you want to purchase a textbook this is the one that I would recommend as a first choice.
There are powerpoint slides available on-line to supplement this text book.
Bioinformatics Algorithms: An Active Learning Approach is an enhanced electronic textbook developed by the author of the course text. You can access some free videos and Powerpoint slides.
Rosalind is a platform for learning bioinformatics through problem solving.

Arthur M. Lesk (2002) Introduction to Bioinformatics, Oxford University Press.

An electronic copy of this book is available from the Queen's Library .
Other books that I have on my desk are:
Wing-Kin Sung (2010) Algorithms in Bioinformatics: A Practical Introduction, CRC Press
Pavel A. Pevzner (2001) Computational Molecular Biology: An Algorithmic Approach

Homework

There will be a new homework assignment almost every week. Open the PDF for the homework due date.
Homework 1.
Homework 2.
Homework 3.
Homework 4.
Homework 5.
Homework 6.
Homework 7.
Homework 8.

Course Description

Calendar Description of CISC-471

Advanced computational approaches to the problems in molecular biology. Techniques and algorithms for sequence analysis and alignment; molecular databases; protein structure prediction and molecular data mining.

Prerequisites: CISC-271/3.0, CISC-352/3.0, CISC-365/3.0, BCHM 218/3.0 (or MBIO-218/3.0), BIOL-334/3.0 (or BCHM-315/3.0).

This course is required in the Biomedical Computing (BMCO) program.

My Description of CISC-471(David Rappaport)

Advances in computer hardware and algorithmic techniques have opened many avenues of inquiry that are driven by computation. The fields of Biology and Medicine are two high profile examples where stunning scientific breakthroughs have occurred within the past few years. In this course I will follow the course text An Introduction to Bioinformatics Algorithms by Neil C. Jones and Pavel A. Pevzner by reviewing standard algorithmic techniques and how they are applied to scientific discovery in biology and bioinformatics. The emphasis will be on the strengths and limitations of these techniques.

Learning outcomes

Knowledge of state of the art algorithms in Bioinformatics with emphasis on the strengths and limitations of these techniques.
Ability to distill information provided by a biologist and discern appropriate and effective algorithmic solutions.
By the end of the course students should be able to:
critically assess an algorithm for its correctness and efficiency, and argue about the algorithms correctness, performance bounds, and approximation ratio as appropriate
obtain an ability to make sensible pragmatic algorithmic choices of standard packages or implementations for specific applications

Outline and Schedule

Chapters numbers correspond to Neil C. Jones and Pavel A. Pevzner (2004) An Introduction to Bioinformatics Algorithms, MIT Press.

Week 1: Jan. 5-9 - Introductory topics. Chapters 1-3.
Week 2-3: Jan. 12-23 - Exhaustive search, branch and bound. Chapter 4.
Week 4-5: Jan. 26- Feb. 6 - Greedy algorithms. Chapter 5.
Week 6-7: Feb. 16 - 27 - Dynamic programming, sequence alignment Chapter 6.
Week 8-9: March 2-13 - Divide and conquer, sequence alignment Chapter 7.
Week 10-12 March 16 - April 3. To be discussed, and review.

The topics covered this year will be similar to last year, but may differ slightly at times. You can see a fairly detailed record on last year's web page: http://research.cs.queensu.ca/~cisc471/2014W/
The following table will be updated as the term progresses.

Suffix Tree
Monday Wednesday Thursday
Week 1
Introduction. 		January 4
Introduction/ Finding most frequent k-mers
Watch this video: The Search for Hidden Messages in the Replication Origin (Part 1). In particular near the 10 minute mark he discusses different approaches to solve the most frequent k-mer problem. Homework 1.
January 5
Finding most frequent k-mers, continued. Review of Big-Ο, Big-Ω, Big-Θ 		January 7
Making Change See Section 2.3 of the text.
Week 2
Exhaustive Search. (Chapter 4) 		January 11
Be prepared to share your homework solutions in class. 		January 12
Restriction Mapping. See section 4.1-4.3 of the text. Homework 2.
January 14
Motif finding. See section 4.4-4.9 of the text.
Week 3
Exhaustive Search. (Chapter 4) Greedy Algorithms (Chapter 5) 		January 18
Motif finding, using branch and bound, and a greedy algorithm. 		January 19
Homework 3.
Be prepared to share your homework #2 solutions in class 		January 21
Genome Rearrangements See section 5.1-5.3
Week 4
Greedy Algorithms (Chapter 5) and Dynamic Programming Algorithms (Chapter 6) 		January 25
Genome Rearrangements See section 5.4-5.5 		January 26
Be prepared to share your homework #3 solutions in class Homework 4. Due February 8.
 January 28
Breakpoint Reversal performance analysis, Intro to dynamic programming algorithms.
Week 5
Dynamic Programming Algorithms (Chapter 6) 		February 1
Quiz #1. I will test your knowledge of material that is related to Homeworks 1 - 3. Please try to arrive early so that you can start the quiz at 11:30 sharp. The duration of the quiz is 50 minutes. 		February 2
Making Change, Dynamic Programming Algorithm. Edit distance and sequence alignment. 		February 4
Solutions to Quiz #1. Edit distance and and sequence alignment, Chapter 6 sections 6.4-6.5 Homework 5. Due February 22.
Week 6
Dynamic Programming Algorithms (Chapter 6) 		February 8
Be prepared to share your homework #4 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. 		February 9
Global sequence alignment and scoring alignments sections 6.6 and 6.7. 		February 11
Local sequence alignment section 6.8
Reading week
 February 15
 February 16
 February 18
Week 7
Dynamic Programming Sequence Alignment (Chapter 6) 		February 22
Be prepared to share your homework #5 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. 		February 23
Alignment with Gap Penalties.
I have prepared an example
that illustrates an algorithm that performs global alignment with affine gap penalties.
Homework 6. 		February 25
Multiple Alignment (see section 6.10)
Week 8
Divide and Conquer (Space efficient Sequence Alignment) 		February 29
Quiz #2. I will test your knowledge of material that is related to Homeworks 4 - 5. Please try to arrive early so that you can start the quiz at 11:30 sharp. The duration of the quiz is 50 minutes. 		March 1
Space efficient sequence alignment.
 March 3
DNA sequencing, Shortest Superstring Problem, Traveling Salesman Problem.
DNA sequencing presentation.
Week 9
Graph Algorithms 		March 7
Be prepared to share your homework #6 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. 		March 8
Sequencing by Hybridization, Euler tours
Homework 7. 		March 10
Euler tours
Week 10
Combinatorial Pattern Matching Suffix Tree 		March 14
Suffix tree, Suffix trie 		March 15
Be prepared to share your homework #7 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. 		March 17
Homework 8.
Week 11
 March 21
 March 22
Be prepared to share your homework #8 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. 		March 24
Week 12
 March 28
Quiz #3. I will test your knowledge of material that is related to Homeworks 6 - 8. Please try to arrive early so that you can start the quiz at 11:30 sharp. The duration of the quiz is 50 minutes. 		March 29
 March 31

Grading

Grades will be made up of classroom participation, midterm quizzes and a final. Assigned homework will include some programming exercises. A large component of the course will involve students solving assigned problems in class.
In class participation: 15%
Three in class midterm quizzes, each worth 15%, total: 45%
Final exam: 40%
The quizzes will be scheduled as follows:
Quiz 1: Monday Feb. 1.
Quiz 2: Monday Feb. 29
Quiz 3: Monday March 28.
Please note the use of a calculator will not be needed and will not be permitted for any of the quizzes. Quizzes will be held in Class.

The final exam for the course this winter will take place as follows:
DATE: APRIL 8, 2016
TIME: 2:00 - 5:00
LOCATION: Goodwin HALL room 247 (our classroom)
All components of this course will receive numerical percentage marks.The final grade you receive for the course will be derived by converting your numerical course average to a letter according to Queen's Official Grade Conversion Scale:

Numeric Range Letter Grade GPA
90-100 A+ 4.3
85-89 A 4.0
80-84 A- 3.7
77-79 B+ 3.3
73-76 B 3.0
70-72 B- 2.7
67-69 C+ 2.3
63-66 C 2.0
60-62 C- 1.7
57-59 D+ 1.3
53-56 D 1.0
50-52 D- 0.7
0-49 F 0

Location and Timing of Final Examinations

As noted in Academic Regulation 8.2.1, "the final examination in any class offered in a term or session (including Summer Term) must be written on the campus on which it was taken, at the end of the appropriate term or session at the time scheduled by the Examinations Office." The exam period is listed in the key dates prior to the start of the academic year in the Faculty of Arts and Science Academic Calendar and on the Office of the University Registrar's webpage. A detailed exam schedule for the Fall Term is posted before the Thanksgiving holiday; for the Winter Term it is posted the Friday before Reading Week, and for the Summer Term the window of dates is noted on the Arts and Science Online syllabus prior to the start of the course. Students should delay finalizing any travel plans until after the examination schedule has been posted. Exams will not be moved or deferred to accommodate employment, travel /holiday plans or flight reservations.

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Students are responsible for familiarizing themselves with the regulations concerning academic integrity and for ensuring that their assignments conform to the principles of academic integrity. Information on academic integrity is available in the Arts and Science Calendar (see Academic Regulation 1 ), on the Arts and Science website (see Academic Integrity ), and from the instructor of this course. Departures from academic integrity include plagiarism, use of unauthorized materials, facilitation, forgery and falsification, and are antithetical to the development of an academic community at Queen's. Given the seriousness of these matters, actions which contravene the regulation on academic integrity carry sanctions that can range from a warning or the loss of grades on an assignment to the failure of a course to a requirement to withdraw from the university.

Accommodation Statement

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