WINONA STATE UNIVERSITY
PROPOSAL FOR NEW COURSES
Department ____Computer Science______________________________
___468_______
Course No.
Date ____3/29/05______
____Algorithms in Bioinformatics ________
Course Name
This proposal is for a(n)
___X__ Undergraduate Course
___3___
Credits
______ Graduate Course
Applies to:
___X__ Major
___X__ Required
______ Elective
Prerequisites
____CS 341, CS 368 and BIOL 310_______________________________________
Grading method __X____ Grade only
______ Minor
_____ Required
_____ Elective
______ P/NC only
______ University Studies*
____ Grade and P/NC Option
Frequency of offering ___every other year______
*For University Studies Program course approval, the form Proposal for University Studies Courses must also be completed and
submitted according to the instructions on that form.
Provide the following information (attach materials to this proposal):
A.
Course Description
1.
2.
3.
4.
5.
6.
B.
Rationale
1.
2.
3.
C.
Statement of the major focus and objectives of the course.
Specify how this new course contributes to the departmental curriculum.
Indicate any course(s) which may be dropped if this course is approved.
Impact of this Course on other Departments, Programs, Majors, or Minors
1.
2.
D.
Catalog description.
Course outline of the major topics and subtopics (minimum of two-level outline).
Basic instructional plan and methods.
Course requirements (papers, lab work, projects, etc.) and means of evaluation.
Course materials (textbook(s), articles, etc.).
List of references.
Does this course increase or decrease the total credits required by a major or minor of any other department? If so, which
department(s)?
List the departments, if any, which have been consulted about this proposal.
University Studies Course Proposals
The form Proposal for University Studies Course must also be completed and submitted according to the instructions on that
form.
Attach a Financial and Staffing Data Sheet.
Attach an Approval Form.
Department Contact Person for this Proposal:
____Mingrui Zhang__________________________
Name (please print)
_507-457-2980__
Phone
mzhang@winona.edu
e-mail address
A.
Course Description
1.
Catalog description.
CS 468 – Algorithms in Bioinformatics 3 S.H.
Theory-oriented approach to the design and analysis of contemporary algorithms, and their applications to
bioinformatics. This course offers an exposition of the algorithmic principles driving advances in the field of
bioinformatics. Data modeling, algorithm design techniques such as dynamic programming and divide-andconquer, and machine learning algorithms are discussed in the contexts of genomics and proteomics. Credit will
only be given for one of CS 440, CS 468, and CS 469.
Prerequisite: CS 341, CS 368 and BIOL 310.
2.
Course outline of the major topics and subtopics (minimum of two-level outline).
I. Introduction
a) Review of fundamental biology concepts for bioinformatics
i. Genes and the genetic code
ii. Transcription, translation, and protein synthesis
b) Overview of computer algorithms for solving bioinformatics problems
II. Data Representations
a) Table, list, heap, stack and tree
b) Data as maps and sequences
c) Mapping and Phylogeneics
i. Physical mapping of DNA
ii. Restriction site mapping, hybridization mapping
iii. Phylogenetic trees
III. Algorithms and Their Complexity
a) The RAM model of computing
b) Time and space complexity, Big-O notation
c) Algorithm design techniques
i. Exhaustive search
ii. Branch-and-bound algorithms
iii. Greedy algorithms
iv. Dynamic programming
v. Divide-and-conquer algorithms
vi. Randomized algorithms
vii. Machine learning
d) Tractable versus intractable problems
e) Sequence alignments
i. Comparison of two sequences
ii. General and affine gap penalty functions
iii. Comparing multiple sequences
iv. Sequence searching statistics and significance
f) Fragment assembly of DNA
i. The biological process of DNA sequencing
ii. Shortest common Superstring
iii. Reconstruction
iv. Multicontigs
IV. Advanced Topics
a) Gene recognition and prediction
i. Gene structure and open reading frame
ii. Algorithms and techniques
b) Proteomics
i. The protein folding problem
ii. Branch and bound techniques for protein threading
iii. Protein structure prediction
c) Microarray Analysis
d) Genetic Algorithms
V. A project on a chosen field of bioinformatics.
3.
Basic instructional plan and methods.
This course needs to strike a balance between practical computer algorithms and their applications to
bioinformatics, emphasizing the ideas underlying computer algorithms rather than offering a collection of
apparently unrelated problems and their solutions. Following the introduction to the theories of computer
algorithms and their designs, their applications need to be discussed. Guest speakers may be invited to give talks in
their expertise areas.
Students will apply the theories covered in class in a major project, and make presentations to the class. Student
project during the class period may lead to either a capstone project or research project later. Appropriate field
trips, e.g., to Mayo Clinic’s Genomics Center, may be arranged for students.
4.
Course requirements (papers, lab work, projects, etc.) and means of evaluation.




5.
Course materials (textbook(s), articles, etc.).



6.
Two exams to assess student’s understanding of fundamentals (40%)
A set of 3-4 smaller projects for student to get hand-on experience with computer algorithms. (20%)
A major term-project (30%)
o Instructor helps student to identify a problem, and to develop a computer algorithm for solving
the problem.
o Group project of 2-3 students.
o 25 minutes oral presentation.
Research paper presentation. (10%)
Jon Kleinberg and Eva Tardos, Algorithm Design, Addison-Wesley, 2005.
Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT Press, 2004.
Software: Perl, Matlab with Bioinformatics toolbox.
List of references.




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William Smyth, Computing Patterns in Strings, Addison-Wesley, 2003.
Pavel A. Pevzner, Computational Molecular Biology: An Algorithmic Approach, MIT Press, 2nd edition,
2001.
D. E. Krane and M. L. Raymer, Fundamental Concepts in Bioinformatics, Benjamin Cummings, 2002.
Peter Clote, Rolf Backofen, Computational Molecular Biology: An Introduction, John Wiley & Sons,
Ltd., 2000
Gusfield, D., Algorithms on Strings, Trees and Sequences -- Computer Science and Computational
Biology. Cambridge University Press, Cambridge, (1997).
Videos:

B.
20th Century with Mike Wallace: The DNA Revolution, History Channel.
Rationale
1.
Statement of the major focus and objectives of the course.
This course is taught to students with interests in the design of computer algorithms for solving
bioinformatics related problems. The algorithms to be developed are data-oriented, where the data is the
huge magnitude of DNA and protein sequences. Computer algorithms need to be adapted before their
applications. As such, bioinformatics provides an excellent environment, as well as examples, for discussing
design issues of computer algorithms.
2.
Specify how this new course contributes to the departmental curriculum.
Bioinformatics is a rapidly growing interdisciplinary area. The increase in the computational aspects of the
field makes bioinformatics an excellent example for presenting and discussing algorithm designs with regard
to DNA and protein sequences. The course will broaden student knowledge about the data-driven algorithms
and their designs for solving real-world problems.
Computer Science is broadening to include areas of emphases related to other disciplines. This course will serve
the course requirements for the Bioinformatics track.
3.
Indicate any course(s) which may be dropped if this course is approved.
None.
C.
Impact of this Course on other Departments, Programs, Majors, or Minors
1.
Does this course increase or decrease the total credits required by a major or minor of any other department? If so, which
department(s)?
This course is not required by any other major or minor.
2.
List the departments, if any, which have been consulted about this proposal.
Biology at RCTC and WSU, and Mathematics at WSU.
WINONA STATE UNIVERSITY
FINANCIAL AND STAFFING DATA SHEET
Course or Program_____CS 468_______________________
Include a Financial and Staffing Data Sheet with any proposal for a new course, new program, or revised program.
Please answer the following questions completely. Provide supporting data.
1.
Would this course or program be taught with existing staff or with new or additional staff? If this course would be taught by
adjunct faculty, include a rationale.
Existing staff will cover this new course.
2.
What impact would approval of this course/program have on current course offerings? Please discuss number of sections of
current offerings, dropping of courses, etc.
This course is part of the new CS curriculum being proposed. In the new curriculum, some existing courses are
eliminated, existing course content is reorganized, and some courses no longer require multiple sections per semester.
Thus, we will be able to offer this new core course every other year.
3.
What effect would approval of this course/program have on the department supplies? Include data to support expenditures for
staffing, equipment, supplies, instructional resources, etc.
No impact.
WINONA STATE UNIVERSITY
APPROVAL FORM
Routing form for new and revised courses and programs.
Course or Program____CS 468________________________
Department Recommendation
_________________________________
Department Chair
________________
Date
Dean’s Recommendation _____ Approved
_________________________________
Dean of College
A2C2 Recommendation
_____ Disapproved
________________
Date
_____ Approved
_____ Disapproved
_________________________________
Chair of A2C2
________________
Date
Graduate Council Recommendation
(if applicable)
_____ Approved
_________________________________
Chair of Graduate Council
________________
Date
_________________________________
Director of Graduate Studies
________________
Date
Faculty Senate Recommendation
_____ Approved
_________________________________
President of Faculty Senate
_____ Disapproved
_____ Disapproved
________________
Date
Academic Vice President Recommendation _____ Approved
________________________________
Academic Vice President
Decision of President
_____ Approved
_________________________________
President
____________________________________________
e-mail address
_____ Disapproved
________________
Date
_____ Disapproved
________________
Date
Please forward to Registrar.
Registrar
_________________
Date entered
Please notify department chair via e-mail that curricular change has been recorded.