Bioinformatics & Proteomics/ Genomics : Introduction to Bioinformatic Computation

MUO course #: BIPG 610 - 3 cr

Prerequisites: BIPG 510/710 - Fundamentals of BPG (recommended)

Offered: Spring semester, Tu/Th afternoons

Course director:  Dr. Alexei Fedorov, Dept. of Medicine, Director of Bioinformatics Lab, (419) 383-5270, Alexei.Fedorov@utoledo.edu


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 to biological and medical students who may lack a background in computer sciences. Programming will be taught using important biological examples. This course focuses in particular on PERL because it is easy to acquire and is the most commonly-used language used in genomics and database analysis. Since UNIX is the dominant platform in present-day 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. 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. advanced use of key desktop applications (local BLAST, CLUSTALW, etc.);
4. database management;
5. object-oriented programming.
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Grading: The course grade will be determined by performance on the midterm project (50%), activities and commitment during labs (30%), and the final exam (20%).

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: Schwartz & Christiansen, Learning Perl (3rd ed) and The Perl Cookbook (2nd ed), O’Reilly http://www.oreilly.com/catalog/lperl3/

Example of previous syllabus: BIPG 610 Syllabus, Spring 2005 (file in PDF format)

Link to course page for registered students: not available at present