BINF 634 Fall 2016 Bioinformatics
Programming
Note material for the course will be provided via GMU Blackboard.
Note course questions will be coordinate using piazza (https://piazza.com/)
Instructor - Dr.Jeff
Solka (jlsolka@gmail.com)
Meeting Place -
Prince William, Colgan Hall 304B
Meeting Time - 4:30-7:10 pm Mondays
Course Webpage
http://binf.gmu.edu/~jsolka/fall16/binf634/Fall_2016BINF_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 or instructor permission.
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.
–
Grading will be on the following scale. 93-100 (A), 90-92
(A-), 87-89 (B+), 80-86 (B), Below 80 C. Student averages
will be
rounded to the closest integer to determine final letter grades.
Projected Class Schedule
August
29, 2016
A Brief Review of Bioinformatics and a Very Brief
Introduction to PERL
Lecture 1 Slides
For Next Week
Read Tisdall chapters 1-5.
Be ready to ask questions
Be ready to answer questions
HW 1: Write programs as described in the following exercises from
"Beginning Perl for Bioinformatics" by Tisdall:
4.3, 4.4, 4.5, 5.2, 5.4 and 5.6
For each exercise, create a perl script called exX.Y.pl, for example,
ex4.3.pl for the first exercise.
Submit these via Blackboard
Sept.
5, 2016
No
class Labor Day
Sept.
12, 2016
PERL Functionality
Lecture 2 Slides (ppt)
snippets2.pl
NM_021964fragment.pep
QUIZ # 1
PROGRAM # 1
Assigned
Assignment
# 1
fasta.pl
genes.fsa
cp_out.txt
test1.fsa
test1.ot
test2.fsa
test2.ot
test3.fsa
test3.ot
Due September 28, 2015 at 7:00 pm via Blackboard
HW #2:
Read Chapter 6
Read Appendix B, pages 315-334, 340-343
Submit exercises 6.1 and 6.2
Sept.,
19 2016
PERL Subroutines
Lecture 3 Slides
(ppt)
Sept.
26 2016
String Functions, Random Number Generation, Hashes, and DNA
Transcription
Lecture 4 Slides
(ppt)
QUIZ # 2
PROGRAM # 1
Due
PROGRAM # 2
Assigned
Assignment
# 2
October
3, 2016
Regular
Expressions
lab1
Slick Regular
Expression Tester code
Oct.
11, 2016
Note
we are meeting on Tuesday of this week at the usual place and time.
Hashes
and Sorting
QUIZ # 3
Oct.
17, 2016
PROGRAM # 2
DUE
In
class MID
TERM EXAM
Oct. 24, 2016
Two
Dimensional Arrays/Complex Data Structures and Parsing
PROGRAM # 3
Assigned
PubMed
File
Oct.
31, 2016
Modules and
Maps
CGI Programming
QUIZ
# 4
Nov.
7, 2016
MySQL
Program
3 Due
Program
4 Assigned
Nov.
14, 2016
Data
Visualization
Lab
2
Nov.
21, 2016
Advanced
Topics: BioPERL, JOINS, ...
Nov.
28, 2016
CMD
Line Recursion and XML
PROGRAM
# 4
Due
TAKE HOME
FINAL
ASSIGNED
Dec.
5, 2016
Python
Perl and R
Review
Dec.
19,
2016
No
Final Exam Given All Late Assignments Due by 7:30 pm
TAKE HOME FINAL DUE