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

Representations and Algorithms for Computational Molecular Biology

Spring quarter, 2000

Time: Tues/Thurs 1:30-2:45 lectures.
Location:  Thorton, Room 102
Televised section:  Thornton 102, Channel E3, Friday 10:00-10:50
Videotape: Located in Terman Library
Internet:  MIS 214 Course by streamed internet video online on Stanford Online
General Course Information
Course Reader:  Will be available at Stanford Bookstore sometime during the course, contents of last year's reader are summarized here.


Schedule of Lectures (HTML table)

Assignments and Projects

Check your grades here

  • Assignment 0:  Class survey.  DUE at NOON on MONDAY, April 3.
  • Assignment 1:  Surfing the Web for Biological Data, DUE at NOON on WEDNESDAY April 5.
  • Project 1:  Dynamic Programming.DUE at 11:59 on MONDAY April 17.
  • Assignment 2:  Sequence Analysis. DUE at the beginning of class THURSDAY April 13.
  • Assignment 3:  Hidden Markov Models. DUE at 11:59pm on THURSDAY April 27.
  • 3-hour Midterm Exam: DUE at noon on WEDNESDAY, May 3.
  • Assignment 4:  Gene Finding & Functional Annotation. DUE at 11:59pm on THURSDAY May 11.
  • Project 2:  Threading and Distances. DUE at midnight on THURSDAY May 18.
  • Project 3:  Microarray-based Gene Classification. DUE at midnight on THURSDAY June 1. (OK to hand in 6/6 w/o using late days)
  • Final Exam:  (Same format as Midterm) DUE at midnight on TUESDAY June 6.  (Can't be late!).
  • Final Course Evaluation:  DUE at Midnight on WEDNESDAY June 7.
  • Lecture Notes and Suggested Readings
  • March 28 (ALTMAN):  Introduction to Bioinformatics & Computational Biology

    • Other Links For Course.

    General Course Information

    Instructors:

    Russ Altman, Associate 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:

    Josh Stuart, stuart@smi.stanford.edu, 650-725-3398
    Office Hours: Monday and Friday 4-5,  at MSOB 215.

    Soumya Raychaudhuri,  sxr@smi.stanford.edu, 650-725-3398
    Office Hours: Monday and Friday 4-5,  at MSOB 215.
     

    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 (approximately 30%), long projects (approximately 50%), midterm and final (approximately 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 7 "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 0 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 7 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.   Students may choose any programming language, but we strongly recommend considering a high level prototyping language for speed of implementation, such as Python, PERL, or others.

    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.