CSE P590A,  Sp '13:  Computational Biology (Professional Masters Program)

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Administrative  Schedule & Reading Course Email/BBoard  Subscription Options  Class List Archive  GoPost BBoard Homework  1:  Assignment  2:  Assignment  3:  Assignment  4:  Assignment  5:  Assignment      Electronic Turnin Lecture Notes  1:  Introduction; Bio Basics  2:  Alignment; DNA Replication    Smith-Waterman Example (.xlsx)  3:  BLAST; Scoring; DNA Sequencing    Daniel's Assembly Slides  4:  MLE & EM    EM Example (.xls)  5:  Motifs; Gene Regulation  6:  HMMs    HMM Example (.xls)  7:  Gene Finding; Splicing  8:  RNA Function & Structure  9:  RNA Search & Discovery  10:  Phylogeny Lecture Recordings  1: Help  2: Apr 11  [get .zip]  3: Apr 18  [get .zip]  4: Apr 25  [get .zip]  5: May 2  [get .zip]  6: May 9  [get .zip]  7: May 16  [get .zip]  8: May 23  [get .zip]  9: May 30  [get .zip]  10: Jun 6  [get .zip] Previous Versions  CSEP 590B, 2011  CSEP 590A, 2008  CSEP 590A, 2006  CSE 590TV, 2003 Resources  Pubmed  NCBI Science Primer  NHGRI Talking Glossary  ORNL Genome Glossary  A Molecular Biology Glossary  BLAST  Swiss-Prot  PDB

Lecture:  MGH 231 (schematic) Th 6:30- 9:20    Office Hours Location Phone Instructor:  Larry Ruzzo, ruzzocs  By appt. CSE 554  (206) 543-6298 TA:  Daniel Jones, dcjonescs  By appt. Course Email: csep590a_sp13@uw.edu. Staff announcements and general interest student/staff Q&A about homework, lectures, etc. The instructor and TA are subscribed to this list. Enrolled students are as well, but probably should change their default subscription options. Messages are automatically archived.  Discussion Board: Also feel free to use Catalyst GoPost to discuss homework, etc. Catalog Description: An introduction to the use of computational methods for the understanding of biological systems at the molecular level. Prerequisite: None Credits: 4 Learning Objectives: The availability of the complete genome sequences of humans and other organisms is one of the landmark achievements of science. Understanding this enormous volume of data is a problem that will challenge scientists for decades to come, and the nature and scope of the problem means that computer scientists will play a vital role. The primary objective of the course is for students to understand the variety of computational problems and solutions that arise in this interdisciplinary field. Students will learn enough of the basic concepts of molecular biology to understand the context for the computational problems presented in the rest of the course. They will learn how some of the computational methods they have encountered in other courses can be applied to solve problems in modern molecular biology. An important component is to learn the nature and capabilities of some of the key public databases available for the solution of these problems, as well as publicly available computational analysis tools and the algorithmic principles underlying them. Late Policy: In general, assignments are due at or before the start of class on the assigned date. The occasional assignment turned in a day or two late is not a problem, but I will start deducting points beyond that. Contact me if you get in a bind this way. Extra Credit: Assignments may include "extra credit" sections. These will enrich your understanding of the material, but at a low points per hour ratio. Do them for the glory, not the points, and don't start extra credit until the basics are complete. Textbook: Richard Durbin, Sean R. Eddy, Anders Krogh and Graeme Mitchison, Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids, Cambridge, 1998.  (Available from U Book Store, Amazon, etc.)  Errata. References: See Schedule & Reading Portions of the CSE P590A Web may be reprinted or adapted for academic nonprofit purposes, providing the source is accurately quoted and duly credited. The CSE P590A Web: © 1993-2013, the Authors and the Department of Computer Science and Engineering, University of Washington.

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