Biochemistry 218 - Biomedical Informatics 231

Doug Brutlag

Course Description

Computational Molecular Biology (Biochem 218) is a practical, hands-on approach to the field of computational molecular biology. The course is recommended for both molecular biologists and computer scientists desiring to understand the major issues concerning representation and analysis of genomes, sequences and proteins. Various existing methods will be critically described and the strengths and limitations of each will be discussed. There will be practical assignments utilizing the tools described. While no computer experience or programming skills are required, prior exposure to personal computers, e-mail, and the Internet are essential. All homework and coursework must be submitted electronically. Prerequisites include an introductory molecular biology course at the level of Biology 41 or permission of the instructor. Students who have not had a course in molecular biology may acquire the necessary background by reading either Stryer's Biochemistry (5th edition by Berg, Tymoczko and Stryer) or Lewin's Genes IX.

Course Requirement

There will be 7 homework assignments utilizing the tools described in the lectures. All homework and final projects will be submitted in electronic form, as e-mail or e-mail attachments. A final paper will be required for the course that critically and constructively analyzes one of the areas presented in the course. The final project may also present a novel application of existing tools or the development of some new or improved method. The final projects will be due Friday, May 30, 2008. There will be no extensions of this deadline. The homework will count for 35% of the final grade and the project will count for 65%.

Examples of Previous Final Projects

 Academic Year 2007-2008

The course will be available online only during the Academic year 2007-2008, via the SCPD web site. You may register for the course Autumn, Winter or Spring quarters.

Registration

Registration is limited to 50 students. On campus students must register with the registrar via AXESS.  Off campus students must register with the Stanford Center for Professional Development.Students receiving a grade of B or better in this course may use this grade as partial completion towards the Stanford Bioinformatics Certificate program.

Auditors

Anyone on Stanford Campus or participating in Stanford Overseas Campus may audit the lectures on the Internet via Stanford Online during a quarter this course is being taught. All lectures are recorded and made available via streaming video (see below for instructions). There is no limit on the number of auditors. Stanford Online lectures are available 24 hours a day, 7 days a week. The only requirement is that the auditors must have a valid SUNET ID in order to view the lecture. Auditors will also be permitted to attend the classes as long as there are seats available. No homework will be permitted and no grade will be awarded for auditors.

Teaching Assistants and Staff

Lee Kozar (kozar@stanford.edu) is the Associate Director of the Bioinformatics Resource at Stanford and is in charge of the computing facilities including software and databases that will be used for the homework. Questions concerning the programs, databases and other computing resources used in the course should be addressed to him.Kimberley Latta (klatta@stanford.edu) is the Administrator for the course. You should contact her for all administrative needs such as registration priority, web page problems, student status, etc.

Lecture Syllabus