Course Description: Three hours lecture. Essential programming skills for computational biology.
Problem-solving and use of specialized bio-computing libraries.
(Credit will not be given to students matriculating in Computer Science,
Computer Engineering , or Software Engineering degree programs.)
Course Objectives: This course is designed to give life scientists
the programming skills needed to analyze, transform, and publish biological
data. No programming experience is required, but students should have basic
computer skills. At the conclusion of the course, students should have basic
proficiency in the use of Perl and have been introduced to BioPerl and other
Perl libraries.
Lecture: Monday Wednesday 3:30 - 4:45 Butler 104
Instructor: Susan Bridges, bridges@cse.msstate.edu
Office: Butler 312, tel. 662-325-7505
Office hours: Tuesday 2-3, Thursday 3-4
Textbook:
James Tisdall, Beginning Perl for Bioinformatics, 2001, O'Reilly &
Associates.
Additional References:
Randal L. Schwartz, Tom Phoenix Learning Perl 3rd Edition, July
2001, O'Reilly & Associates.
CGI Programming 101 available on-line
Larry Wall,
Tom Christiansen, Jon Orwant, Programming Perl, 3rd ed., July 2000, O'Reilly
& Associates. (July 2000).
David Till, Teach Yourself Perl 5 in 21
days available online
Course schedule: See schedule
Assignments: See assignments
Grading:
Students taking the course for graduate credit will have extra requirements on the
programming assignments and course project.
Grading is on a 10 point scale.
Attendance: Students are expected to attend all classes. If you must
be absent, you should notify the instructor ahead of time if possible. More than
3 unexcused absences will result in a reduction of one letter grade in the
course. Students who are auditing the course must attend all lectures. An audit
will not be awarded if a student has more than 3 unexcused absences.
Academic honesty policy: Cheating on homework or a quiz will result in
an F on the assignment and cheating on an exam will result in an F for the
course as well as possible university disciplinary measures. A student must cite
any references used in or resources used to complete homework, projects and term
papers. Failure to properly cite references can result in a grade of 0 on the
assignment. You may ask other students for assistance in debugging your
programs, but the program should be your own work. You will learn almost nothing
in this class if you do not do the assignments yourself. See the Computer Science
Departmental Policy Regarding Professional Conduct. The University policy
regarding academic honesty applies to all MSU students.
Add/drop policy: See the Mississippi State
University Add/Drop Policy
