Introductory Biomedical Informatics

Biomedin 202

Course Coordinators: Russ Altman, Larry Fagan, Betty Cheng

The class consists of a series of lectures which are designed to introduce the breadth and scope of biomedical informatics. This course is for those without previous programming or biological/medical exposure but who wish to obtain sufficient background to follow progress in the field. Since there are close to 60 hours of lectures available, students may select some topics to suit their interests. Some topics in medical informatics and bioinformatics are basic and necessary in order to followed the advanced lectures: these are the required lectures listed below. You should indicate your area of interest (medical informatics vs. bioinformatics) and view the required lectures in that topic. You must choose at least 10 lectures to obtain credit for the class. Once you have completed the required lectures, you are free to choose advanced lectures in the same area or choose lectures from other topics to bring the total to 10. Study is self-paced, lectures are offered online and a short assessment, which covers the required lectures from your chosen area only, is given.

1 unit

Offered Aut, Win, Spr, Sum

Location: All lectures are available over the Internet

Contact Larry Fagan (lfagan @ stanford.edu) or Betty Cheng (bcheng @ stanford.edu) for instructions about the course and to obtain the username and passwords needed to view the lectures.

An orientation session will be offered at the beginning of each quarter. Please attend this session to receive your username and password. Drs. Fagan and Cheng will be present to answer questions about the course and to assist with selection of lectures to suit your interests. If you cannot attend the orientation session, contact either Dr. Fagan or Cheng to receive instructions.

Next orientation session: Friday, January 11, 2008, 12:00 PM, in MSOB x-263 .

Time: Self-paced study

Pick One of these two sets of Lectures as your Focus

1) Bioinformatics Class Topics

  • Pairwise Sequence Alignment using Dynamic Programming
  • Sequence Alignment using BLAST
  • Multiple Sequence Alignment
  • Discovering the Function of Proteins and Proteomes
  • Microarray Data Analysis: Clustering and Classification Methods
  • Microarray Analysis with the Stanford Microarray Database
  • Molecular Visualization

OR

2) Medical informatics Class Topics

  • Introduction to Medical Informatics
  • Bibliographic Retrieval
  • Controlled Clinical Terminologies & Informatics Standards
  • Introduction to Electronic Medical Records (EMR)
  • Privacy & Security
  • Automated Systems for Decision Support I
  • Medical Imaging Informatics

Supplementary Material

The level of both sets of lectures is introductory but the Bioinformatics class assumes some knowledge of biology. To help everyone get started with prerequisite material, both Larry Fagan and I have created some "courselets", small sets of lectures devoted to essential prerequisite information for our field. To view the complete list of courselets, see: http://scpd.stanford.edu/scpd/courses/courselets/list_auth.asp

Recommended Textbooks - Bioinformatics

"Molecular Biology of the Cell" is a useful basic biology textbook written by Alberts, et. al. The first six chapters are most essential for the bioinformatics portion of the class. The four biology courselets cover the most significant material from these chapters using the fourth edition.

"Bioinformatics" by David Mount is the textbook best suited for the topics & teaching approach for the bioinformatics half of the class. Unfortunately, this text doesn't cover functional genomics very well as this area experienced significant growth after the publication date. "Bioinformatics and Functional Genomics " by Jonathan Pevsner covers functional genomics but the treatment of sequence alignment and protein structure doesn't mesh well with the approach taken by the lecturers. For the purposes of this course, it's best to borrow these textbooks, if possible.

Recommended TextBooks - Medical Informatics

Medical Informatics by Shortliffe et. al. is the textbook for the Medical Informatics portion of the course. The second edition is adequate for these lectures (3rd is the latest edition). (http://www.dbmi.columbia.edu/shortliffe/textbooks.shtml)

Use Axess to sign up for the course for a grade.

Please contact Larry Fagan (lfagan @ stanford.edu) or Betty Cheng (bcheng @ stanford.edu) for instructions about how to get access to the lectures or questions.

Report problems with this webpage to Betty Cheng.