BINF 734 Advanced Programming

Term Every Spring

Book

No textbook is required, but portions of the class are printed in:
Python for Bioinformatics, J. Kinser, Jones & Bartlett, 2009

Pre-requisites

The student should have some programming experience in a language like C++, Java, or Matlab. Knowledge of Python is not required as this language will be taught at the beginning of the semester. Students should also a foundation in linear algebra.

Overview This course will create programs for algorithms commonly used in bionformatics. These algorithms include dynamic programming, genetic algorithms, principal component analysis, and clustering. These programs will be applied to real problems. As the semester progresses the course will also consider recent publications in bioinformatics and replicate them in part.

Style of Class

This class will require a significant amount of programming. In fact, there is no final or midterm. The grade is almost completely based on the programming and a project.

The semester will begin with the basics of Python and some useful modules. The class will then explore common algorithms and construct codes for them. These programs will be applied to recently published cases.

The types of algorithms and cases may change according the research interests of the students.

Syllabus for Spring 2012

• Jan. 24: Intro to the course and Python.
• Jan. 31: Program to read Genbank files.
• Feb. 7: Alignments, arrays, and numpy.
• Feb. 14: Dynamic Programming.
• Feb. 21: Multiple Alignments.
• Feb. 28: Clustering
• Mar. 6: PCA
• Mar. 13: SPRING BREAK
• Mar. 20: Text Mining
• Mar. 27: Trees
• Apr. 3: Skew
• Apr. 10: ngrams
• Apr. 17: New topic - dependent on class preference
• Apr. 24: New topic - dependent on class preference
• May 1: Presentations

Honor Code All GMU students abide by an honor code. Students in this class will do their own work and write their own programs.