HORT 503
BIOINFORMATICS FOR RESEARCH
SPRING 2012
Credits: 2
Goals
The course will:
1. Provide a general overview of bioinformatic tools for use in research.
2. Provide hands on training of bioinformatic tools customized to individual students
research activities.
3. Promote skills in critical thinking.
4. Promote skills in research communication.
5. Promote scientific teamwork.
Instructor
Dr. Dorrie Main, 45 Johnson Hall, 335 2774, dorrie@wsu.edu
Best by appointment (email me), but if my door is open, just pop in.
Class time
Wednesday/Friday 1.10 –2.50 pm, Johnson Hall Room 24
Course website
www.bioinfo.wsu.edu/teaching/Hort503
Prerequisites
A laptop
Text book
No prescribed text, materials will be provided
Expected student learning outcomes
Through engagement in lectures, assignments, and other activities, students will:
1. Demonstrate an understanding of the correct use of bioinformatic tools in sequence
analysis and individual research projects.
2. Demonstrate teamwork, problem-solving, and communication skills.
COURSE OUTLINE
Date
Jan
24
29
Topic
Student Introduction Presentations, Introduction to Bioinformatics Movie,
Course Syllabus Review
Terminology Fundamental Presentations and Discussion, Overview of Case
Studies
Genomics and Bioinformatics Review, Literature Searching, Database Resources
Overview and Exercises.
Sequence Alignment and Comparative Genomics Overview and Exercises
Gene Prediction, Genome Annotation and Genome Browsers Overview and
Exercises
Enabling Technologies Presentations and Discussion, Sequence Analysis Exercises
Genome and Transcript Assembly Overview, Case Study and Exercises
Genome Resequencing, Marker and Primer Identification Overview and Exercises
Multiple Sequence Alignment, Domain Prediction, Phylogenetic Analysis
Overview and Exercises
Structural Bioinformatics Overview and Exercise
Other Bioinformatics Tools Overview
02
07
09
Class Project Presentation
Projects
Project Presentations, Class Summary and Evaluations
25
27
Feb
01
03
08
10
15
17
22
Mar
ASSESSMENT
Total = 100 pts
10
5
10
10
25
40
Assignment 1 – Introduction to Bioinformatics Research Exercises
Assignment 2 – Terminology Fundamentals Presentation
Assignment 3 – Enabling Technologies Presentation
Assignment 4 – Genome Annotation Exercise
Assignment 5 – Bioinformatics Solutions Team Project
Assignment 6 – How Bioinformatics Can Enable My Research
Grading scale
100-93%
90-92%
86-89%
83-85%
80-82%
A
AB+
B
B-
76-79%
73-75%
70-72%
66-69%
62-65%
< 62
C+
C
CD+
D
F
Late assignments – Written reports are due at the beginning of class on their due date. Late
assignments will result in a 10% grade penalty per day beginning the first day the assignment
was due.
Assignment briefs
1. Introduction to Bioinformatics Research Exercises 1 -3 due January 25 (10% of grade).
2. Terminology Fundamentals Presentation due January 27th (5% of grade).
3. Enabling Technologies Presentation due Friday February 10th (10% of grade)
4. Genome Annotation Exercise due February 17th (10% of grade)
5. Class Project Presentation due March 02 (25% of grade)
6. Individual Project Report and Presentation due March 9th (40% of grade)
Attendance
Attendance is expected and may sometimes be recorded. Attendance and participation in class
sessions will be encouraged and may influence the course final grade. Absences because of
illness, personal and/or family crises, mandated court appearances, university approved events,
or similar reasons will be accommodated as long as such absences are not excessive and
notification is provided to the instructor in advance. Excused absences should be arranged
prior to any known or planned event. Required University activities will be excused absences if
an official Class Absence Request form signed by the sponsoring faculty or organization is given
to the instructor before the event.
Disability statement
Reasonable accommodations are available for students who have a documented disability.
Please notify the instructor during the first week of class of any accommodations needed for
the course. Late notification may cause the requested accommodations to be unavailable. All
accommodations must be approved through the Disability Resource Center (DRC) in
Administration Annex 206 (Tel. 335-1566).
Cheating (WAC 504-25-310)
Cheating is the intentional use of, or attempt to use, unauthorized material, information, or
study aids in any academic activity to gain advantage. Cheating includes, but is not limited to,
communicating improperly with others, especially other students, during tests or the
preparation of assignments for classes; copying from books, notes, or other sources during a
test when this is not permitted; copying from another student’s work (reports, laboratory work,
computer programs, files, etc.); making improper use of calculators or other devices during a
test; illegitimately procuring or using copies of current examinations; allowing a substitute to
take an examination or write a paper for oneself.
Plagiarism (WAC 504-25-310)
Plagiarism is knowingly representing the work of another as one’s own, without proper
acknowledgment of the source. The only exceptions to the requirement that sources be
acknowledged occur when the information, ideas, etc., are common knowledge. Plagiarism
includes, but is not limited to, submitting as one’s own work the work of a “ghost writer” or
work obtained from a commercial writing service; quoting directly or paraphrasing closely from
a source without giving proper credit; using figures, graphs, charts, or other such material
without identifying the sources.
Academic Integrity Processes (WAC 504-25-315)
Every act of academic dishonesty affects academic evaluation of the student and also is a
violation of the University’s standards of conduct. Responsible instructors retain the authority
and responsibility to assign grades to students, considering from an academic standpoint the
nature of the student’s action. This is the case even when the case is referred to the University
Academic Integrity Process. Students have recourse to appealing the responsible instructor’s
assignment of grades according to usual academic policy. See Academic Regulation 104.
All clear instances of academic dishonesty shall be reported to the Office of Student Conduct as
outlined in 504-35-335(2). The first reported instance at WSU of academic dishonesty by a
student will be treated as purely an academic matter unless, in the judgment of the responsible
instructor, more serious action should be taken through the disciplinary process. Any allegation
of subsequent academic dishonesty will be treated as a matter to be referred to the Office of
Student Conduct
Reports of Academic Dishonesty (WAC 504-35-320)
Any member of the University community who witnesses an apparent act of academic
dishonesty shall report the act either to the instructor responsible for the course or activity or
to the Office of Student Conduct.