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The departments of Biological Sciences and Computer Science at San Jose State University designed a new BSCS Track in Bioinformatics.

Prerequisite Courses Molecular Biology for Computer Scientists Biology 23 Offered in Spring 2008 Tuesdays and Thursday: 2:30 - 3:45, DH 415. Instructor: Dr. Brandon White The aim of this course is to help computer science students become familiar with the principles of molecular biology as they relate to bioinformatics. The emphasis will be on the molecular workings of a cell, including the fundamental processes by which coded genetic information is decoded during the production of useful macromolecular structures and machines. The course is a prerequisite for CS students who want to take Bioinformatics I, Bio/CS 123A, to be offered in Fall 2008. Prerequisites: CS 46A and CS 46B; No college biology required. Introduction to Computer Science for Biologists and Chemists CS 23 Not offered in Spring 2008 This course is an introduction to computer science topics needed to enter the field of bioinformatics and is open to Biology/Chemistry students. Simple C and Perl programming in a Unix environment and basic database access techniques will be covered. The course is an in-lab course and serves as the prerequisite for a joint Bio/CS 123A course. Prerequisites: Bio 5 or Chem 55, or instructor approval; no prior knowledge of computer programming required.

Required Courses Bio/CS 123A Next time offered: Fall 2008 Instructor: Dr. Sami Khuri This practical course, cross-listed with the biology department, provides an introduction to the main public domain tools, databases and methods in bioinformatics, including DNA and protein databases, such as Genbank and PDB, software tools such as BLAST, FASTA, Smith-Waterman; and methods including those for aligning sequences. More precisely, the course analyzes the algorithms behind the most successful tools, such as the local and global sequence alignment packages mentioned above; and the underlying methods used in fragment assembly packages. This course is intended both for biology and computer science students, to work together to solve complex biological questions requiring modification of standard code. Prerequisites: Bio 23 for Computer Science students or instructor approval. Bio/CS 123B Offered in Spring 2008. Tuesdays and Thursday: 9:00 - 10:15, DH 450. Instructor: Dr. Sami Khuri This practical course, cross-listed with biology, continues to cover the computational methods used for searching, classifying, analyzing, and modeling protein sequences. The course also continues to cover tools for analyzing DNA and RNA sequences. More advance topics, such as genetic algorithms and simulated annealing which can be used to address folding problems, are covered. Prerequisites: Bio/CS 123A or instructor approval.

Overview of the program