WINONA STATE UNIVERSITY
PROPOSAL FOR NEW COURSES
Department ____Computer Science______________________________
Date ____3/29/05_____________
___368________________
Course No.
____Introduction to Bioinformatics________________________
Course Name
This proposal is for a(n)
___X__ Undergraduate Course
____3________
Credits
______ Graduate Course
Applies to:
__X____ Major
__X___ Required
__X___ Elective
Prerequisites
_____CS 250_and BIOL 241______________________________________________________________________
Grading method __X____ Grade only
______ Minor
_____ Required
_____ Elective
______ P/NC only
_____ University Studies*
____ Grade and P/NC Option
Frequency of offering ___Once a 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:
____Chi-Cheng Lin__________________________
Name (please print)
___(507) 285-7145________
Phone
clin@winona.edu
e-mail address
A.
Course Description
1.
Catalog description.
CS 368 Introduction to Bioinformatics – 3 S.H.
This course introduces students to the fundamental concepts of bioinformatics. Topics include introduction to
DNA machinery and informatics, pairwise sequence alignments, bioinformatics programming, bioinformatics tools
and database searches, genomics and proteomics, and introduction to DNA microarray analysis.
Prerequisite: CS 250 and BIOL 241.
2.
Course outline of the major topics and subtopics (minimum of two-level outline).
 DNA’s Information Content
o Overview of bioinformatics
o Central dogma of molecular biology
o Information storage in DNA and genetics code
 Sequence Alignment
o Dynamic programming
o Pairwise sequence alignments
 Global sequence alignment
 Local sequence alignment
 Gaps in sequence alignment
 Bioinformatics Databases
o Biological databases
 Gene databases
 Protein databases
o Sequence search
 Programs and algorithms
 BLAST
 FASTA
 Bioinformatics programming and tools
o Specific programming language, as needed – e.g., Perl
 Introduction to language
 Arrays and hashes
 File I/O and control structures
 Functions and subroutines
o Regular expression and substitution patterns
o BioPerl
o Other tools of molecular biology
 Genomic Information Content
o Phylogenetics
 Cluster analysis
 Parsimony approaches
o Prokaryotic and eukaryotic genomes & gene structures
o Gene recognition
o Gene expression
o Introduction to microarrays
 Proteomic Information Content
o Predicting RNA secondary structure
o Protein secondary structure
o Protein folding
o Structural modeling and visualization
o Proteomics, protein classification and modification
3.
Basic instructional plan and methods.
This class is lecture/discussion based. In addition, computer labs will be used to demonstrate and study
bioinformatics databases and tools. Programming projects will be used to reinforce the algorithms and concepts
studied in the class. One or two guest speakers may be invited to present their research in this field.
4.
Course requirements (papers, lab work, projects, etc.) and means of evaluation.
The evaluation for this course will be based on exams, programming projects, homework assignments, and lab
reports. The class will include one midterm exam and a final exam. The programming assignments will be done
using the Perl programming language.
5.
Course materials (textbook(s), articles, etc.).
Texts:
Fundamental Concepts of Bioinformatics, by Dan E. Krane and Michael L. Raymer, published by Benjamin
Cummings, 2002.
Beginning Perl for Bioinformatics, by James Tisdall, published by O'Reilly, 2001.
6.
List of references.
An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), by Neil C. Jones and Pavel A.
Pevzner, published by the MIT press, 2004.
Structural Bioinformatics, by Philip E. Bourne (Editor), Helge Weissig (Editor), published by Wiley-Liss, 2003.
Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, by Dan Gusfield,
published by Cambridge University Press, 1997.
DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, by Pierre Baldi and G.
Wesley Hatfield, published by Cambridge University Press, 2002.
Microarray Bioinformatics, by Dov Stekel, published by Cambridge University Press, 2003.
Mastering Perl for Bioinformatics, by James D. Tisdall, published by O’Reilly, 2003.
Genomic Perl: From Bioinformatics Basics to Working Code, by Rex A. Dwyer, published by Cambridge University
Press, 2002.
Articles from National Center for Biotechnology Information (NCBI) Web site: http://www.ncbi.nih.gov/ .
B.
Rationale
1.
Statement of the major focus and objectives of the course.
The primary objective of this course is to introduce students to the fundamental concepts of bioinformatics.
Bioinformatics is an emerging field that uses computational tools and computer technologies to model, analyze,
process, store, retrieve, manage, present, and visualize biological data, particularly the genomics and proteomics
data. This interdisciplinary course will also provide students with the opportunities to apply computer
technologies to solving real-world problems.
2.
Specify how this new course contributes to the departmental curriculum.
Computer Science is broadening to include areas of emphases related to other disciplines. This course will fit into
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 and Mathematics Departments, as well as RCTC’s Biology Department.
WINONA STATE UNIVERSITY
FINANCIAL AND STAFFING DATA SHEET
Course or Program_____CS 368_______________________
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 course.
Initially, this course will be offered only on the Rochester campus, with ITV to Winona as necessary. In addition, we will
make use of the expertise in this field in Rochester in the form of guest lecturers and adjunct co-instructors, as
appropriate.
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 each year.
It will also count as an elective for existing majors and will be offered alternately with other electives.
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.
The support of an adjunct professor and/or invited speakers will be helpful, if possible.
WINONA STATE UNIVERSITY
APPROVAL FORM
Routing form for new and revised courses and programs.
Course or Program____CS 368________________________
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.