The University of Toledo

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 2013

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
BPG Program
3rd Floor CCE Building
Mail Stop: 1034

EDUCATIONAL PROGRAM OBJECTIVES (EPO's) for Computation Course

A BPG Graduate Student Will Be Knowledgeable
In the course of their educational program, students are provided the opportunity to gain knowledge through instruction by content experts and by supervised participation in research projects.  Knowledge will be assessed by the student’s ability to define, describe, and explain facts and concepts, as well as at higher levels of cognition that will be measured by the ability to apply, analyze, and integrate content.

Before graduation, a student will have demonstrated to the satisfaction of the faculty:

K1.  Knowledge of fundamental systems biology technologies, such as proteomics, genomics and transcriptomics.

K2.  Knowledge of algorithmic and statistical methods for analysis of nucleic acid and protein sequences, such as hidden Markov models and Bayesian statistics.

K3.  Knowledge of at least one modern computer programming language, such as PERL.

A BPG Graduate Will Be Skilled
The BPG curriculum provides a training environment in which research and teaching skills are learned in concert
with the correlated knowledge.  Students have the opportunity to gain these skills under the supervision of a faculty
mentors with the advice and guidance of the student advisory committee, through direct contact with content and/or
technical experts, and through direct participation in research projects. 

Before graduation, a student will have demonstrated to the satisfaction of the faculty:

S1.  The ability to perform procedures necessary for the completion of the student’s thesis (M.S.) research project(s).

S2.  The ability to perform research productively as an individual or member of a research team.

S3.  The ability to use electronic databases via automated scripting.

S4.  The ability to retrieve biomedical information for solving problems that are relevant to the appropriate completion of a research project, and accurate reporting of the results.

A BPG Graduate Will Be Professional
The University of Toledo College of Medicine and the Biomedical Sciences Program recognize the importance of role-modeling and directly training the professional conduct and character of its students.  The institution and the BPG Track devote curricular and extracurricular time to the development of ethical standards humanistic and professional behaviors by its students. 

Before graduation, students will have met the following institutional and program standards:

P1.  Respect for, and adherence to, all laws & regulations governing ethical use of computers and remote computational facilities.

P2.  Respect for, and adherence to, the principles and legal responsibilities that govern responsible conduct of research.

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