(4 Units, Spring quarter)
Time: Tues/Thurs 1:15-2:30, Monday evenings 8-9:15
Location: Gates Building, Room B01
Videotape: Available at Math/CS Library
Schedule of Lectures (HTML table)
Schedule of Lectures (GIF format)
Assignments and Projects in PDF format
Lecture Notes and Suggested Readings
Instructors:
Russ Altman, Assistant Professor of Medicine (and Computer Science, by courtesy), Section on Medical Informatics. MSOB X-215, Stanford, Mail Code 5479. 725-3394, altman@smi.stanford.edu
John Koza, Consulting Professor of Computer Science and Symbolic Systems, Gates Building 258, Stanford, Mail Code 9020, 723-1517, koza@cs.stanford.edu
Co-instructors:
Volker Brendel, Department of Mathematics (volker@grendel.stanford.edu)
Douglas Brutlag, Department of Biochemistry (brutlag@cmgm.stanford.edu)
Peter Karp, SRI International (pkarp@ai.sri.com)
Michael Levitt, Department of Structural Biology (levitt@hyper.stanford.edu)
Jeanette Schmidt, Polytechnic University (jschmidt@smi.stanford.edu)
Teaching Assistants:
Richard Chen, rchen@smi.stanford.edu, 3-2990
Liping Wei, wei@smi.stanford.edu, 5-3399
Office Hours to be determined.
Course Coordinator: Kevin Lauderdale, MSOB X215, (415) 725-0659, kxl@smi.stanford.edu
Description:
This course will introduce the basic computational issues and methods used in molecular biology, combining core lectures, programming assignments, and guest lectures. In addition, the course will introduce and use biological data sources available on the world wide web media. Topics will include basic algorithms for alignment of biological sequences and structures, as well as more advanced representational and algorithmic issues in structure and sequence computation. These include, for example, dynamic programming algorithms for alignment, structural superposition algorithms, simplified representations, probabilistic representations of structural uncertainty, hidden Markov models, Bayesian networks, statistical feature detection, genetic algorithms, constraint satisfaction and minimum description length encoding. The guest lectures will, in part, showcase different computational approaches being pursued by different research groups in several departments at Stanford.
We will assume no previous biology background. We will assume an interest in biology, however.
Units: This course is for 4 units. It can be taken for 3 units by arrangement with instructors. A lecture-only, no assignment participation may be taken for 1 unit by arrangement with instructors.
Grading: The course will be graded solely upon 2-3 programming projects and approximately 4-6 short exercises. There is no midterm or final.
Auditors: Must be approved by Dr. Altman.
Prerequisites: Matrix mathematics and programming skills required. Familiarity with biology helpful, but not required. The CS requirement is meant to ensure that people can write computer programs, and understand the basics of data structures and algorithms. The math requirement is meant to ensure that people feel comfortable with matrix algebra.
Computer resources: You will need to have access to email on the internet. In particular, we will use a WWW browser (forms-compatible), such as Netscape. All of these resources are available to Stanford students at Sweet Hall and elsewhere. All course material will be placed on the WWW in *.pdf (Adobe Acrobat) format, which allows the documents to be read on multiple platforms. Readers are available for free for Windows, Macintosh and many unix platforms at the Adobe website.
Course readings: Will be distributed as needed in class, or through the course coordinator. Assignments and Projects will be made available electronically only.
