Biomedical Informatics 214 (also listed as Computer Science 274) Representations and Algorithms for Computational Molecular Biology Spring 2002 Note this is not the current year website, this is for archival purposes only. Click here for the current year's website.

Lectures: Thornton 102, Tues/Thurs 1:30-2:45PM, Channel E2
Sections: Thornton 102, Friday 10:00-10:50AM, Channel E1
Videotape: Located in Terman Library
Internet: BMI 214 Course by streamed Internet video online on Stanford Center for Professional Development

Table of Contents

See old announcements in the archive.

• May 27th:
  1. Information about the final:

  * It will be a open book test.
  * It will be available from 9am Tues June 11 to 3am Wed June 12th (this includes the time slot normally allocated to our class meeting time)
  * It will cover lectures from April 30 to end of course
  * It will be generally the same format and rules as Midterm
  * It will not be possible to use late days without special prior approval (which we do not want to grant, generally), because we need to get final grades to the registrar, and so using late days is a problem that may lead to an INCOMPLETE, depending on the details...
  

  2. Information about grades:

  * We use a curve in grading, and in the past, it has been considered somewhat generous. Thus, you should not spend time computing your total % points, as it will not enable you to predict your grade, unless you know everyone else's grades.
  * We think that generally people are doing very well in this class, even with a homework or project that does not get all the points, so most of you should feel good about your efforts.
  * It is best to use email to ask for clarifications of homeworks, and to visit the TAs in their office hours for more detailed
  questions/debates/comments.

Instructor:

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

Tiffany Jung
MSOB X215, 650-725-0659

Allison Waugh  650-725-3398
Office Hours:  Fridays 11am-noon (MSOB [251 Campus Dr.], x215)

Iwei Yeh   650-725-3398
Office Hours:  Mondays 10am-11am (MSOB [251 Campus Dr.], x215)

Zhen Lin   650-725-3399
Office Hours:  Wednesdays 4pm-5pm (MSOB [251 Campus Dr.], x215)

Mailing Lists: (top)

• staff: bmi214-staff@smi.stanford.edu (This is the best way to reach us.)
• students: bmi214-students@smi.stanford.edu

To subscribe:
send email to majordomo@smi.stanford.edu
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where youremail@xxx.stanford.edu should be your email address

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send email to majordomo@smi.stanford.edu
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Description: (top)

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: (top)

• This course is normally taken 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.  Students must attend all lectures, absences must be approved by the instructors

Grading: (top)

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: (top)

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) and must be requested prior to the due date. No late day is allowed after Final Exam.

Partner Policy: (top)

for assignments:
Students may discuss and work on problems in groups but must write up their own solutions. When writing up the solutions, students should write the names of people with whom they discussed the assignment.

for programming projects:
Students may discuss ideas with others. However, programs are to be completed independently and should be original work.

Auditors: (top)

Must be approved by Dr. Russ Altman.

Prerequisites: (top)

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: (top)

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.

Required Course Textbook: Available at Stanford Bookstore. We have also placed copies of the textbooks on reserve at the Lane Medical Library and Math/CS library. (top)

Mount, D.W., Bioinformatics : sequence and genome analysis. 2001, Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press. xii, 564. ISBN: 0879696087.

We also suggest students to read through classic articles in bioinformatics/computational biology (scanned).

Note on courses in computational biology: (top)

BMI 214 (also listed as CS 274) is this course. It has been taught since 1996 and is an introduction to representations and algorithms for analysis of sequence, structure and function. It requires programming skills and aims to give an understanding of the biological problems that arise, and how algorithms are developed to address them. It does not train students to be expert users of tools, but gives them an in-depth knowledge of some tools and a broad introduction to the technical issues in analysis of biological data. It is taught live on Tuesdays/Thursdays and is also on Stanford Online.

Biochem 218 (also listed as BMI 231) is Doug Brutlag's course introducing computational molecular biology, also a number of years old. It is more geared towards gaining an expert understanding of existing tools and databases, and as such complements BMI 214 very nicely. There is no programming required. Most students take both eventually and learn a lot--even the areas where there is overlap are presented differently enough to round out one's understanding. For logistical reasons this course is also being taught on Tuesdays/Thursday and is on Stanford Online. It is usually offered in the Winter live, and in all quarters on Stanford Online, but the schedule was changed this year.

CS 262 (Computational Genomics) is Serafim Batzoglou's new course. It will focus principally on algorithms for sequence assembly, analysis and comparison. It will have a strong CS algorithms and data structures component, probably with an element of software engineering as well. It is likely to complement both courses, although in the future, about 1/3 of BMI 214 may overlap sufficiently to require coordination--the part about sequence and string analysis. The coordination has not been done as of now, however. It does not contain much on 3D structure computation and functional computing, judging from the syllabus. The course will be taught live, and most likely on Stanford Online (ask Prof. Batzoglou).