Requirements

• Prerequisites: Bioinformatics I, BIOI 7711, with a grad of B or higher, or permission of the instructor.
• Knowledge of molecular biological concepts
• Significant experience in computer sciences
• Ability to read and understand primary scientific literature
• Access to a computer with internet connection and the ability to write programs and accomplish your course project. Some computational resources may be available in the Computational Bioscience space of the Barbara Davis Center
• A willingness to participate in promiscuous paired programming and other forms of extreme programming
• Knowledge or ability to rapidly learn C/C++, PERL, R, MySQL, Apache, PerlGD, and a little bit of PhP and Java

Reading and Textbooks : Recent research publications will be drawn from conferences such as the Pacific Symposium on Biocomputing (PSB) and the conference on Intelligent Systems for Molecular Biology (ISMB) and journals such as PLoS Computational Biology, Bioinformatics, Genetics, Genome Research, Nature, Science, etc. Course readings will be made available on-line by the individual instructors.

There is no required textbook, but the following books (available at the bookstore or Amazon.com) are recommended:

• Bioinformatics: Sequence and Genome Analysis by David Mount
• Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids by Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison.
• Computer Modelling by Andrew Leach
• Extreme Programming Pocket Guide by chromatic.

Research Topics: To be announced; will depend on individual instructors.

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