Computational Tools for Bioninformatics
COSC 576
(Tuesdays, 5:30-6:45, PH303, Thursdays on-line (emuonline.edu)
Instructor: Matt
Evett ; Dept. Computer Science; Pray-Harold 512E
Tel: 734-487-1227;
e-mail: evett@emunix.emich.edu;
www.emunix.emich.edu/~evett/BioinformaticsTools; webcaucus.emich.edu (the COSC576_W05
caucus).
Office Hours: TTh 10-12, W 1-2:45.
You may drop by at times other than office hours, but in that case I cannot
guarantee that I'll be able to see you.
Prerequisite: An introductory programming course,
such as COSC238 or COSC514.
Textbooks:
Course Summary: An introduction to tools for programming and data management
commonly used in bioinformatics. Topics include Perl programming, bioinformatics
programming libraries for Perl and Java, web and data markup languages, and
database technology (database design and queries). The course is project oriented,
with Perl and maybe some Java programming assignments spread throughout the
semester.
Course Calendar:
Due dates for projects are underlined. Exam
dates are in bold. Holiday dates are italicized.
| Date |
Text:Topic |
Projects/Exams due |
| Week 1 |
Chapter 2: Installing Perl |
|
| Week 2 |
Ch3 Basic flow-of-control |
|
| Week 3 |
Ch 4: Sequences, strings, arrays, hashes. |
|
| Week 4 |
Ch 5: blocks & subroutines |
|
| Week 5 |
Ch.6 & 7: File IO, Patterns |
|
| Week 6 |
Ch. 8 & 9: Data sets
From Mastering Perl: Ch 1,3:
Modules, classes, autoloading |
|
| Week 7 |
Ch 10: Protein Data Bank |
|
| Week 8 |
Ch. 12: Biological databases |
|
| Week 9 |
Ch.12 & 13 Perl & databases (DBI) |
Midterm Exam |
| Week 10 |
Ch 14, 15: Perl & the Web |
|
| Week 11 |
Ch16, 17: BLAST & microarrays |
|
| Week 12 |
Ch 17: Tools & Datasets (BLAST, etc.) |
|
| Week 13 |
Ch 17, 18: More datasets |
|
| Week 14 |
Ch 19: Visualization |
|
| Week 15 |
Ch 20: Bioperl (time permitting) |
|
| 4/22, 5:30 |
|
Final Exam, regular room |
Grading Policy:
The final course grade will be a weighted average of the grades received in each
of the following categories, as specified: Small projects & homeworks 5%,
Programs 45%, Midterm exam 20%, Final exam 30%.
Tardiness Policy: Programming and other homework assignments
will be due at the beginning of class. After that, assignments will
be accepted through the start of the next scheduled class, but will suffer
a full grade penalty. E.g., if a late programming assignment is worthy
of an 'A', I will mark it a 'B'. Assignments more than one class late will
not be accepted, and will receive a grade of 'F'.
Attendance Policy: We're all grown-ups, when and whether you attend
class is up to you. However, missed assignments, and exams shall only be excused
by a doctor's written note, verifying that the student was medically indisposed
to attend class that day.
Grading of Programs: Grading of programming assignments will
reflect three factors, weighted as shown.
-
(70%) Correctness -- does the program run correctly.
-
(15%) Style -- does the code adhere to class documentation standards? Is
the code indented properly? Are the variable names mneumonic? How well
has the student followed the basic formatting characteristics for the language?
-
(15%) Design -- is the program adequately decomposed (i.e., are the functions
and procedures small enough to be comprehensible)? Are the class and structure
definitions well chosen? How well has the student taken advantage of the
language's capabilities?
Announcements and the Web Page:
Students should view the course web page regularly for announcements regarding
programming assignments, readings, etc. I update course web pages frequently!
Cheating policy:
Students are required to attend to the policy
on academic dishonesty outlined in the EMU student handbook. In addition,
collaboration among students in solving programming and homework assignments is
forbidden. If I receive programs or homework assignments that are substantially
equivalent, or which are not the original work of the student submitting the material,
I will not hesitate to punish all involved parties to the fullest extent, up to
and including assignment of a failing grade for the course, and referral to the
Office of Judicial Student Services for
possible punitive action at the University level, which may include expulsion
from the University. In addition, the University and the computer science department
maintain policies regarding proper behavior on its computer systems. Failure to
adhere to these policies can result in loss of computer privileges, and possible
legal action.