BINF 734 Syllabus

throneharshBiotechnology

Oct 2, 2013 (4 years and 9 days ago)

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BINF 734

-

Syllabus

Purpose

The purpose of this class is for the student to gain an understanding of how to create a variety of
programs to perform different bioinformatics tasks. The course will include descriptions of
algorithms and methods by which
these can be implemented into computer codes. This course
will also attempt to replicate some recent bioinformatics publications.


Prerequisites

Previous programming experience is not required but is an advantage. Students with experience
in Java, C/C++, C
\
# or other procedural languages will be able to draw on this experience.


Textbook

Instead of a textbook, this course will rely on recently published papers in bioinformatics.
Students may wish to purchase their own Python reference book.


Instructor:

Ja
son M. Kinser

PW Phone: 703 993 3785

Email: jkinser@gmu.edu

Office hours: Since many students are employed and the instructors office is on another campus,
office hours are made by appointment. Meetings in FFX can be schedule on Wednesdays.
Meetings on t
he other days will be in PW.


Course Pedagogy
:

The best way to learn (and also grade) a programming course is for the students to do a lot of
programming. Therefore, the idea of a traditional mid
-
term/final format does not work for this
course. Instead the

grading in this course is based upon two items:

70% of the grade is based upon the homework,

30% of the grade is based upon a final project


Schedule
:

Jan. 2
5
: Intro to the course and Python.

Feb.
1
: Program to read Genbank files.

Feb
8
: Alignments, arrays, and numpy.

Feb 1
5
: Dynamic Programming.

Feb 2
2
: Multiple Alignments.

Mar
1
: Clustering

Mar 9: PCA

Mar 15
: SPRING BREAK

Mar 2
2: Text Mining

Mar
29
: Trees

Apr
5
: Skew

Apr 1
2
: ngrams

Apr
19
: New topic


dependent on class preference

Apr

2
6
: New topic


dependent on class preference

May
3
: Presentations