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.eduDr. 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

Computations Course Schedule for 2017

Full course syllabus can be found here.

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.

After completion of the Computation course, please click on the above link, print out the Evaluation Form, complete and return anonymously to:

Student Learning Objectives (SLO's) for the Bioinformatics Computation course can be found here.

Jo Anne Gray
BPG Program
3rd Floor CCE Building
Mail Stop: 1034

Last Updated: 6/15/17