Fall_2009BINF_634

BINF 634 Fall 2009 Bioinformatics Programming

Instructor - Dr.Jeff Solka (jlsolka@gmail.com)

Meeting Place - Prince William Ocaquan Building Rm 304B
Meeting Time - 4:30-7:10 pm Mondays

Course Webpage
http://binf.gmu.edu/~jsolka/fall09/binf634/Fall_2009BINF_634_Syllabus_rev1.html

Course Description:

This course will provide an introduction to Bioinformatic Programming using PERL. Some of the topics that will be covered include rudimentary language syntax, hashes, subroutines, two-dimensional arrays, modules, CGI programming, MySQL, visualization, and BioPERL.

Prerequisites:

Rudimentary biological background such as taught in BIOL 482 or the equivalent. Rudimentary programming background such as taught in IT 108 or CS 112 or the equivalent.

Required Text:

Beginning Perl for Bioinformatics by Tisdall and Waliszewski

–Programming Perl (3rd Edition) by Wall, Christiansen and Orwant

Grading:

•Programming assignments (50%)

–5 graded programming assignments

•Exams: Midterm (20%) and Final (20%)

–May include both closed-book section and open-book programming problems

•In-class Quizzes (10%)

•Weekly homework assignments

–All HW assignments must be submitted to me by the beginning of the next class. HW assignments will not be graded individually, but you may be called upon to discuss your work during the next class. Therefore, late assignments will not be accepted.

–

Projected Class Schedule

August 31, 2009

A Brief Review of Bioinformatics and a Very Brief Introduction to PERL

Lecture 1 Slides

Sept. 7, 2009

No class Labor Day

Sept. 14, 2009

PERL Functionality

Lecture 2 Slides (ppt)

Lecture 2 Slides (pdf)

QUIZ # 1

PROGRAM # 1 Assigned

test1.fsa

test1.ot

test2.fsa

test2.ot

test3.fsa
test3.ot

Sept., 21 2009

PERL Subroutines

Lecture 3 Slides (ppt)

Sept. 28, 2009

String Functions, Random Number Generation, Hashes, and DNA Transcription

Lecture 4 Slides (ppt)

QUIZ # 2

PROGRAM # 1 Due

PROGRAM # 2 Assigned

Oct. 5, 2009

Regular Expressions

Lecture 5 Slides (ppt)

Oct. 12, 2009

Hashes and Sorting

QUIZ # 3

PROGRAM # 2 DUE

Lecture 6 Slides (ppt)

Oct. 19, 2009

Two Dimensional Arrays

MID TERM EXAM

Oct. 26, 2009

Complex Data Structures and Parsing

Lecture 7 Slides (ppt)

PROGRAM # 3 Assigned

Nov. 2, 2009

Modules and Maps and CGI Programming

Lecture 8 Slides (ppt)

Lecture 9 Slides (ppt)

QUIZ # 4

Nov. 9, 2009

MySQL

Lecture 10 Slides (ppt)

PROGRAM # 3 Due

PROGRAM # 4 Assigned

Nov. 16, 2009

Data Visualization

Lecture 11 Slides (ppt)

QUIZ # 5

Nov. 23, 2009

Advanced Topics: BioPERL, JOINS, ...

PROGRAM # 4 Due

Nov. 30, 2009

CMD Line Recursion

TAKE HOME FINAL ASSIGNED

Dec. 7, 2008

Review, fun and games.

Dec. 14, 2008

No Final Exam Given All Late Assignments Due

TAKE HOME FINAL DUE