Introduction to Bioinformatics Course Syllabus

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COURSE SYLLABUS
Introduction to Bioinformatics, ONLINE!
school of allied health and life sciences
WELCOME !
COURSE NUMBER:
BSC4434/5459
COURSE TITLE:
Introduction to Bioinformatics
COURSE OVERVIEW:
In order to keep pace with recent developments in genomics and proteomics,
biology must develop and teach new tools so our students will have the skills
to enter this burgeoning job market. As one example, to find out who is
hiring, how much you are worth, and online hiring trends, see
biohealthmatics.com.
Central to these new technologies is bioinformatics, a field that did not exist a
decade ago. No one predicted the collision of two fundamental technologies:
molecular biology and small fast computers. Biology is now publishing more
than 50,000 pages of literature per day. Over 125,000 different genomic
sequences have been submitted to the North American GenBank (the world
wide repository of genetic sequence information database) IN A SINGLE DAY.
10 years ago there were only two bacteria fully sequenced. Now there are
820 fully sequenced life forms, including 152 eukaryotes (one of which is
Homo sapiens), 109 bacteria and more than 550 viruses. We now have full
sequences for the mouse, the fruit fly and brewers yeast. Biologists are
literally in danger of drowning in their own success.
This absolutely necessitates the creation of new tools that allow us to move
through all this information and make some sense of it. This requires very
fast computers, very clever programming and well educated operators. The
field is now known as bioinformatics, and some universities now have whole
Bioinformatics Departments offering Ph.D. programs in this area. It has
become one of the most sought after degrees by the pharmaceutical industry
where all molecular research groups now include one bioinformaticist. Most
NIH and NSF grants to universities dealing with sequence information have a
similar bias.
At UWF, this course is based on a hands-on approach that I hope will develop
your interests in scientific discovery.The course is also structured to involve
you in meaningful ways with practical (and exciting) aspects of real research
in bioinformatics, by showcasing UWF faculty in various modules using
computer-based tools to enhance their research.
What do former students say about this class? Here is one example:
"I listed you as one of my contacts for reference and there is a
professor at LSU's Coastal Fisheries Institute and Department of
Oceanography and Coastal Sciences that [is] interested in me...his
work involves [sic] population modeling. He has told me that his
students do a lot of programming and that he is aware of the work
that I did in Bioinformatics. I really am glad that I took your class
because as it turns out my experiences in that class may help me get
an assistantship..."
COURSE COORDINATOR:
Melanie A. Sutton, Ph.D.
CONTACT INFORMATION:
http://uwf.edu/content/enforced/61035DEVELOP.MelanieSutton.msutton/importantcourseinformation/mailto:msutton
@uwf.edu or (850) 474-2650
School of Allied Helath and Life Sciences, University of West Florida
PREREQUISITES OR COREQUISITES:
Please see the official UWF Catalog.
Computer phobic? Think again...No prior knowledge of programming is
required as a prerequisite. Students will be taught programming
basics in the course and will also have the opportunity to utilize online
tutorial sessions for additional skill development in order to complete
programming assignments in the area of bioinformatics for this course.
Your term project will encompass the implementation of a practical
application in the emerging field of bioinformatics, utilizing your
research/experimental design and numerical analysis/modeling skills. This will
be team-based assignment. Although the initial lab examples will be in the
area of genetics, the course sequence PCB 3063/PCB 3063L: Genetics is not a
required prerequisite for this course unless you (or your team) wish to
develop a project in this area. Alternately, students in previous semesters
have applied the skills developed in this class to create successful projects
encompassing the subfields of ecological, medical, public health, or
pharmaceutical informatics.
COURSE DESCRIPTION:
Please see the official UWF Catalog.
COURSE OBJECTIVES AND STUDENT LEARNING OUTCOMES:
This course meets the following programmatic goals for the Department of
Biology, the Interdisciplinary Information Technology-Bioinformation track
program, and the MSA-Biomedical/Pharmaceutical track program. Upon
completion of this course, students will be able to:
o
o
Integrity/Values:
 Defend use of the IEEE-ACM Software Engineering Code of
Ethics and Professional Practice as it relates to assignements in
this course and development of their team-based term project.
Project Management:
 Defend uses of bioinformatics resources, including software,
database search engines, and other Internet tools.
 Defend uses of data mining and data visualization tools in
informatics research.
 Implement computational procedures and algorithms to analyze
structures and functions of biological systems and systems
related to a term project.
 Program basic methods for digitizing, storing, processing and
displaying information related to informatics applications.
Fulfillment of these goals will be assessed through examinations, a set of
laboratory exercises (with associated online discussion, quizzes, or other
assessment requirements), and completion of a team-based, term project in
the area of bioinformatics. For the purposes of programmatic assessment,
the following mastery levels will be used:
Characteristics of Submitted Student Work and Assignments
SKILL MASTERY
LEVEL
INTEGRITY/VALUES
PROJECT MANAGEMENT
Exceeds
Expectations (Very
Good to Excellent)
Student consistently demonstrates clarity of
Student has a clearly defined sense of the value of
thought process, ability to communicate well with
biomedical/pharmaceutical research and related ethical
team members, and consistently demonstrates
issues. Student can articulate and defend arguments with
abilities and understanding that surpass expected
specificity.
average.
Meets Expectations
(Satisfactory)
Student demonstrates adequate awareness of the value
of biomedical/pharmaceutical research and related
ethical issues. Student can articulate and defend
arguments, but lacks some specificity.
Below Expectations
(Unsatisfactory)
Student demonstrates poor communication skills
Student does not demonstrate adequate awareness of the
with team members or demonstrates a critical
value of biomedical/pharmaceutical research and related
inability to grasp central concepts, execute
ethical issues, or student is unable to articulate and
technologies, or think logically to synthesize
defend arguments with any specificity.
appropriate conclusions.
TOPICS COVERED:
Student has adequate communication skills and
demonstrates basic level of understanding of
project management, however, these abilities
rarely surpass expectations.
Topic
Approximate coverage (all
1.
Designing and maintaining a course website; Clickable image images
4 hours
2.
Beginner's guide to bioinformatics and Perl; Programming strategies
4 hours
3.
Representing and reasoning about sequence data
4 hours
4.
Recap of Perl constructs; Introduction to searching for motifs
4 hours
5.
Practice with subroutines and regular expressions in Perl
4 hours
6.
Simulating a DNA sequence by programming randomization
4 hours
7.
Creating a reusable Perl module
4 hours
8.
Introduction to databases
4 hours
9.
Databases: Case studies in informatics-based research
4 hours
10. Database Issues with implementation in Perl
4 hours
11. Term Project Brainstorming, Milestones, and Defense
4 hours
)
12. A professional code of ethics and professional practice for you as a programmer 4 hours
Total instructional hours
48 hours total (all
)
indicates online course modules that may be completed from home or
using UWF computer labs.
REQUIRED TEXTS/MATERIALS:
Beginning Perl for Bioinformatics by James Tisdall. O'Reilly & Associates.
[ISBN: 0-596-00080-4]. Code examples from your book are also available online. (Please note: Text can sometimes be found for as low as $16 on amazon.com.)
SPECIAL TECHNOLOGY UTILIZED BY STUDENTS: (beyond baseline requirements
of e-mail and word processing)
Students are encouraged to complete this course utilizing the equivalent of a
cable-speed modem. Completing the course modules via a telephone dial-up
connection will require significant download times for larger audio-visual
content.
REFERENCES/BIBLIOGRAPHY:


IEEE-ACM Software Engineering Code of Ethics and Professional Practice
See additional links embedded in modules in eLearning.
GRADING/EVALUATION:
Fulfillment of the programmatic goals described above will be assessed as
follows:
o
o
o
60% Examinations (Midterm Exam and Final Exam, weighted equally)
20% Participation (laboratory exercises and associated assessment)
20% Term Project, including Website (team-based)
Examinations: There will be a midterm and final exam in the course. These
exams will be based on module materials, textbook readings, supplemental
readings, laboratory exercises, and the provided on-line resources.
These exams will include multiple choice, fill-in-the-blank, short answer, and
essay questions.
Participation: Laboratory exercises and associated assessment in the form
of quizzes or discussion participation provide the hands-on component to the
course. In some of these exercises, you will be investigating case studies
related to modern informatics applications, exploring research conducted by
faculty here at UWF, or learning how to use globally accessible databases or
source code. The goal is to motivate you by showing you the excitement of
informatics-based projects, while also helping you to develop a better
understanding of "good" design and algorithmic development which can
impact the larger industrial and research communities. To emphasize the
importance and significance of developing your ability to communicate
scientific information effectively, participation in selected online forum
discussions will be graded using a Discussion Forum Grading Rubric
available in the eLearning course.
Term Project: Students will be assigned to teams including approximately 45 students per team. A list of possible topics in bioinformatics will be
provided, and project brainstorming and milestone discussions will be
scheduled throughout the semester. All final projects will be presented as
Websites, and you will be taught basics of Website design in a course lab.
Part of your grade for this component will include (1) defending your Website
online and (2) providing professional feedback to your classmates.
Information on these requirements will be made available as associated term
project deadlines approach. To help you prepare for this assignment, please
also review the Term Project Guidelines and Examples document when it
is posted, which also contains links to tutorials developed by the UWF Library
to help you prepare your abstract and include professional referencing within
your paper.
Optional Tutorials: Several tutorials will be posted during the first few
weeks of the course for those students with limited computer backgrounds.
These tutorials will cover how to use eDesktop, common programming
errors, how to create a course Website, and how to link assignments on your
new Website.
Calculation of Final Gade: Due to the distance learning nature of this
course, all requirements must be completed within the time scheduled, unless
prior arrangements are made with the instructor. Your final grade will be
determined by the points you accumulate within each category, divided by
the total points available within that category. These scores will then be
weighted based upon the percentages indicated above to determine your final
grade. On-line facilities will be provided so students can monitor their own
progress. The final grade will be on a 10-point scale, roughly: A range = 90100, B range = 80-89, etc., with plus/minus grades as appropriate.
EXPECTATIONS FOR ACADEMIC CONDUCT/PLAGIARISM POLICY:



Academic Conduct Policy [Web]
Plagiarism Policy [
PDF]
Student Handbook [
PDF]
It is the philosophy of The University of West Florida that academic
dishonesty is a completely unacceptable mode of conduct and will not be
tolerated in any form. All persons involved in academic dishonesty will be
disciplined in accordance with University regulations and procedures.
Discipline may include suspension or expulsion from the University. Scholastic
dishonesty includes but is not limited to cheating, plagiarism, collusion, the
submission for credit of any work or materials that are attributable in whole
or in part to another person, taking an examination for another person, any
act designed to give unfair advantage to a student or the attempt to commit
such acts.
In addition, any behavior that interferes with the conduct of a class is
classified as disruptive behavior and will not be tolerated. Although not
exhaustive, examples of disruptive behavior would include: inappropriate or
threatening online postings or e-mails, etc.
QUALITY ASSURANCE:
This course is reviewed for quality by assessment personnel within the School
of Allied Health and Life Sciences (SAHLS) to meet national standards
established by the Southern Association of Colleges and Schools and to
address quality enhancement initiatives of SAHLS.
ASSISTANCE:
Students with special needs who require specific examination-related or other
course-related accommodations should contact Disabled Student Services
(DSS), [email protected]f.edu, (850) 474-2387. DSS will provide the student with a
letter for the instructor that will specify any recommended accommodations.
Every effort will be made to accommodate the special needs of disabled
students. Please inform the instructor privately during the first week of class
to indicate your particular needs. All such accommodations are officially
arranged through the Office for Disabled Student Services and a letter from
this office must accompany your request.
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