Medical Information Sciences 214 (also listed as Computer Science 274)

Representations and Algorithms for Computational Molecular Biology

Spring quarter, 1999

Time: Tues/Thurs 1:15-2:30
Location:  McCullough Building, Room 150
Videotape: Located in Terman Library
Internet:  MIS 214 Course by streamed internet video online on Stanford Online
General Course Information
Course Reader:  Available at Stanford Bookstore, contents summarized here.


Schedule of Lectures (HTML table)

Industrial panel on Bioinformatics took place on  May 12, 6:30-8:00 PM.

David Balaban, Affymetrix, Inc. (david_balaban@affymetrix.com)
Ramon Felciano, Ingenuity, Inc. (felciano@ingsys.com)
Peter Karp, Pangea Systems, Inc. (pkarp@PangeaSystems.com)
Eugeni Vaisberg, Cytokinetics, Inc. (evaisberg@cytokinetics.com)
Michael Walker, Consultant to Incyte Pharmaceuticals, Inc. (walker@smi.stanford.edu)


Assignments and Projects

Check your grades here.

  • Assignment 0:  Class survey
  • Assignment 1:  Surfing the Web for Biological Data
  • Project 1:  Dynamic Programming Sequence Alignment
  • Assignment 2:  Probability, Motif Finding and Multiple Sequence Alignment
  • Assignment 3:  Gene Function Finding and Perl Programming
  • Project 2: Threading and Distances  (DUE: 12:00 NOON, Monday, May 24, Electronic)
  • Project 3: Dihedral Angles and Structure Superposition  (DUE: 12:00 NOON, Wed, June 2, Electronic)
  • Final Exam (DUE: 12:00 NOON, June 8 Electronic)
  • Course Evaluation  (DUE: 12:00 NOON, June 8, Electronic)
  • Lecture Notes and Suggested Readings

    • Other Links For Course.

    General Course Information

    Instructors:

    Russ Altman, Assistant Professor of Medicine (and Computer Science, by courtesy), Stanford Medical Informatics. MSOB X-215, Stanford, Mail Code 5479. 650-725-3394, altman@smi.stanford.edu

    John Koza, Consulting Professor (Medical Informatics), Stanford Medical Informatics, MSOB X-215, Stanford, Mail Code 5479. 650-941-0336, koza@smi.stanford.edu
     

    Teaching Assistants:

    Xiaole Liu, xliu@smi.stanford.edu, 650-725-3398
    Office Hours currently Tue, Thr 5:00-7:00 pm at MSOB 215.

    James Wang, wang@smi.stanford.edu, 650-725-3398
    Office Hours TBA.
     

    Course Coordinator: Kevin Lauderdale, MSOB X215, (650) 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, with midterm and final. 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, computing with distance information, 3D motif definition and computation, hidden Markov models, phylogenetic trees, statistical feature detection, genetic algorithms, design of data resources, automated analysis of biological literature, database integration, and collaborative environments for supporting biology.

    We will assume no previous biology background. We will assume an interest in biology, however.

    Units:

    Grading: The course will be graded by performance on short homeworks (30%), long projects (50%), midterm and final (20%, both take home, open book).

    Late policy:  All projects, assignments and exams should be submitted electronically by the specified time due (Pacific Standard Time).  Each student is granted 10 "free" late days that can be used as extensions for any project, assignment or  exam (exceptions: Midterm Exam can have a max of 3 late days, Final Exam can have a max of 2 late days).  Late days will be measured in 24-hour/day calendar days with no distinction for weekends or holidays, and will be rounded UP to the nearest integer (thus, 10 minutes late = 23 hours late = 1 day late). After you use up all your free days, your grade on late projects/assignments/exams will be reduced 10% for each  late day.  Extensions beyond the 10 free days may be granted at the discretion of the instructor (not the TAs) but must be requested prior to the due date.

    Auditors: Must be approved by Dr. Altman.

    Prerequisites: Previous exposure to 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 and the web to access assignments. All of these resources are available to Stanford students at Sweet Hall and elsewhere. Most 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. A course reader is being prepared (ready 2nd or 3rd week of course).

    Updated virtually continuously by Russ Altman...Thanks to Lee Kozar for background graphic.