bioinformatic computations
UT- BPG course #: BIPG 6100/8100 - 3 cr
Prerequisites: BIPG 5100/7100 - Fundamentals of BPG (recommended)
Offered: Spring semester, Monday/Wednesday afternoons, room 127HEB
Course director: Dr. Alexei Fedorov, Dept. of Medicine, Director of Bioinformatics Lab, (419) 383-5270, Alexei.Fedorov@utoledo.edu. Dr. Fedorov's lab website can be viewed here.
Summary: Bioinformatics is a fundamental component of modern biomedical sciences.
Only computers have the capability to collect, organize, annotate, and process the
enormous amounts of information about the organization and structure of the biosphere.
Familiarity with a computer language is essential to those who seek expertise in bioinformatics.
The main goal of this course is to provide basic programming skills. Programming will
be taught using important biological examples. This course focuses in particular on
PERL, because it is easy to learn and is the most commonly-used language used in genomics
and database analysis. Since UNIX is the dominant platform in computational biology,
students will be made familiar with UNIX environments, including Linux and OSX. Each
registered student will be given an account on the MUO Linux computer cluster, the
most powerful computer within the College. Hands-on programming experience will be
obtained in the Bioinformatics Computer Lab at UT. Students are encouraged to bring
their own problems and projects to work on during this course. In addition to learning
programming and other bioinformatic skills, the students of this course acquire knowledge
in how to present the final product of bioinformatic research and how to write a scientific
paper on the subject. This work resulted in the publication of the articles listed on Dr. Fedorov's lab
website. The major course objectives are to familiarize the student with:
1. Use of UNIX-based operating systems;
2. Use of the PERL programming language in bioinformatic applications;
3. The basic tasks needed to interface with supercomputers
4. Communicating competently with fellow team members in projects
Grading: The course grade will be determined by homework/project: 40%, labs and activities:
20%, Midterm exam: 15%, and the final exam 25%.
Instruction: The course is primarily taught by the course director, with some lectures
from the faculty at the University of Toledo and Bowling Green State University.
Text: No textbooks are required. Students will work with the information/instructions
provided online.
END-OF-COURSE STUDENT EVALUATION FORM:
After completion of the Computation course, please click on the above link, print
out the Evaluation Form, complete and return anonymously to:
Heather Buska
BPG Program
3105G CCE
FULL COURSE SYLLABUS (PDF format) can be found here.
STUDENT LEARNING OBJECTIVES (SLO's) for the Bioinformatics Computation course can
be found here.