Introduction to Bioinformatic Computation
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 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. 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 below.* 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.
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/
Syllabus for Computation Course: BIPG 6100 Syllabus, Spring 2015
END-OF-COURSE STUDENT EVALUATION FORM: please click here (pdf document)
After completion of the Computation course, please click on the above link, print out the Evaluation Form, complete and return anonymously to:
Jo Anne Gray
3rd Floor CCE Building
Mail Stop: 1034