Stanford School of Medicine
Course Catalog–

Biomedical Informatics

27 Courses

Chair and Program Director::
Russ Altman, MD, PhD

Co-Director:
Mark Musen, MD, Ph.D.

Department web site:
http://bmi.stanford.edu/

Steering Committee:
http://bmi.stanford.edu/Directory/

Participating Departments:

Anesthesia
Biochemistry
Biostatistics
Business
Civil and Environmental Engineering
Computer Science
Electrical Engineering
Genetics
Health Research and Policy
Management Science and Engineering
Mathematics
Mechanical Engineering
Medicine
Neurosurgery
Obstetrics and Gynecology
Pathology
Radiation
Radiation Oncology
Radiology
Statistics
Structural Biology
Surgery

Courses given in Biomedical Informatics Program have the subject code BIOMEDIN.

This interdisciplinary program was created in response to a recognized need for well-trained researchers and academic leaders in the expanding field of biomedical informatics. It was formerly called Medical Informatics Sciences (1982-2000).

The program in Biomedical Informatics emphasizes research to develop novel computational methods that can advance biomedicine. Students receive training in the investigation of new approaches to conceptual modeling and to development of new algorithms that address challenging problems in the biological sciences and clinical medicine. Students with a primary interest in developing new informatics methods and knowledge are best suited for this program. Students with a primary interest in the biological or medical application of existing informatics techniques may be better suited for training in the application areas themselves.

GRADUATE PROGRAMS

The Biomedical Informatics Program is interdepartmental and offers instruction and research opportunities leading to MS and PhD degrees in Biomedical Informatics. All students are required to complete the core curriculum requirements outlined below, and also to elect additional courses to complement both their technical interests and their goals in applying informatics methods to clinical settings, biology, or imaging. Students who fail to maintain a 3.0 grade point average (GPA) in all five categories of the core curriculum are expected to pass a comprehensive exam in that area before the graduate degree is granted. In addition, all degree candidates must pass an oral examination that tests the student's ability to integrate the various components of the curriculum and to relate them to the overall field of biomedical informatics.

The core curriculum is common to all degrees offered by the program but is adapted or augmented depending on the interests and prior experience of the student. Deviations from the core curriculum outlined below must be justified in writing and approved by the student's Biomedical Informatics academic adviser and the chair of the Biomedical Informatics Committee. It should be noted, however, that the program is intended to provide flexibility and to complement other opportunities in applied medical research that exist at Stanford. Although most students are expected to comply with the basic program of study outlined here, special arrangements can be made for those with unusual needs or those simultaneously enrolled in other degree programs within the University. Similarly, students with prior relevant training will have the curriculum adjusted to eliminate requirements that were met as part of their prior training.

CORE CURRICULUM

All students are expected to participate regularly in the Biomedical Informatics Student Seminar (BIOMEDIN 201) and Colloquia (BIOMEDIN 200), regardless of whether they register for credit in those courses. In addition, all students are expected to fulfill requirements in the following five categories:

  1. Core Biomedical Informatics (15 units): students are expected to understand current applications of computers in biology and medicine and to develop a broad appreciation for research in the management of biomedical information. Required courses are the three quarter sequence Introduction to BIOMEDIN 210, 211, and 214, all of which should be taken during the first year in the program. Students must also take an additional 3 units of Biomedical Informatics course work (which may include crosslisted courses from other departments, but not including BIOMEDIN 200, 201, 299, 302, or 303), selected in consultation with the academic adviser. BIOMEDIN 212 is strongly encouraged.


  2. Computer Science (9 units): the student is expected to acquire a knowledge of the use of computers, computer organization, programming, and symbolic systems. It is assumed that students will have had by matriculation prior computing experience at least equivalent to a course introducing the fundamentals of data structures and algorithms such as CS 103A,B, 103X, 106A,B, 106X, or other courses approved by academic adviser or executive committee. All students are required to take a minimum of 9 units of courses in the Department of Computer Science. If similar courses have not been taken previously, these units must include CS 121, 161, and a course that requires significant programming and knowledge of machine architectures (for example, EE 182, CS 110, or the CS 193 series). For those who have taken such courses previously, replacement units may be taken from any other course in CS selected by the student and approved by the academic adviser. A course in databases is especially recommended. With the exception of CS 110, all other courses applied to the degree requirements must be numbered 137 or higher.


  3. Probability, Statistics, and Decision Science (9 units): students are required to take at least three courses that span the following five topics: basic probability theory, Bayesian statistics, decision analysis, machine learning, and experimental-design techniques. Prior courses in statistics at least equivalent to STATS 60 and calculus equivalent to MATH 42 are prerequisites. A prior course in linear algebra equivalent to MATH 103 or 113 is recommended. For the probability requirements, students may, for example, take MS&E 120, STATS 116, or MS&E 221. For the statistics requirements, sequences (taken after STATS 116) may include STATS 200 followed by a course in stochastic modeling, machine learning or data mining, such as STATS 202, 215, or 315A,B, or CS 228 or 229. Options for decision analysis include MSE 152 or 252, or cost effectiveness analysis (BIOMEDIN 432). Specific courses should be chosen in consultation with the student's academic adviser. Also recommended is a course in the psychology of human problem solving.


  4. Biomedical Domain Knowledge (9 units): students are expected to acquire an understanding of pertinent life sciences and how to analyze a domain of application interest. Prior courses in biology at least equivalent to BIOSCI 41 and 42 are prerequisites. All students must have completed a course in basic biochemistry, molecular biology, or genetics. Other areas of basic biology may be an acceptable alternative. Exposure to laboratory methods in biology is encouraged. All students without formal health care training must take BIOMEDIN 207.


  5. Social and Ethical Issues (6 units): candidates are expected to be familiar with key issues regarding ethics, public policy, financing, organizational behavior, management, and pertinent legal topics. Students may select at least 6 units from suitable courses that include, for example, BIOMEDIN 250, 256, and 432; CS 201; HRP 390, 391, and 392, or any other advanced course in policy and social issues proposed by the student and approved by the Biomedical Informatics academic advisor.

The core curriculum generally entails a minimum of 46 units of course work, but can require substantially more or less depending upon the courses selected and the previous training of the student. The varying backgrounds of students are well recognized and no one is required to take courses in an area in which he or she has already been adequately trained; under such circumstances, students are permitted to skip courses or substitute more advanced work. Students design appropriate programs for their interests with the assistance and approval of their Biomedical Informatics academic adviser. At least 27 units of formal course work are expected.

PROGRAM REQUIREMENTS FOR THE ACADEMIC MS, PROFESSIONAL MS, AND COTERMINAL DEGREES

Students enrolled in any of the MS degrees must complete the program requirements in order to graduate. Programs of at least 54 units that meet the following guidelines are normally approved:

  1. Completion of the core curriculum.


  2. A minimum of 6 additional units of courses in Computer Science numbered 135 or higher, courses in Management Science and Engineering or Statistics numbered 200 or higher, PSYCH 256 or 267, or relevant courses in other departments approved by the student's academic advisor.


  3. Electives: additional courses to bring the total to 54 or more units.


  4. Teaching: all students are expected to act as Teaching Assistants (TAs) for at least one course during their first two years of training. This will generally be in one of the informatics short courses, although another course approved by the program faculty may occasionally be substituted.

The University requirements for the MS degree are described in the "Graduate Degrees" section of the current Stanford Bulletin.

MASTER OF SCIENCE (ACADEMIC)

This degree is designed for individuals who wish to undertake in-depth study of biomedical informatics. Normally, a student spends two years in the program and implements and documents a substantial project during the second year. The first year involves acquiring the fundamental concepts and tools through course work and research project involvement. All first- and second-year students are expected to devote 50 percent or more of their time participating in research projects. Research rotations are not required, but can be done with approval of the academic adviser or training program director. Graduates of this program are prepared to contribute creatively to basic or applied projects in biomedical informatics. This degree requires a written research paper to be approved by two faculty members.

MASTER OF SCIENCE (PROFESSIONAL)

This new degree is primarily designed for the working professional who already has advanced training in one discipline and wishes to acquire interdisciplinary skills. This program is offered part-time and courses are available online. The professional MS is offered in conjunction with Stanford Center of Professional Development (SCPD), which establishes the rates of tuition and fees. SCPD is based on the honors cooperative model (HCP), which assumes that the student is working in a corporate setting and is enrolled in the MS on a part-time basis. The student has up to five years to complete the program. Research projects are optional and the student must make arrangements with program faculty. Graduates of this program are prepared to contribute creatively to basic or applied projects in biomedical informatics.

MASTER OF SCIENCE (COTERMINAL)

The coterminal degree program allows undergraduates to study for a master's degree while completing their bachelor's degree(s) in the same or a different department. Please refer to the "Coterminal Bachelor's and Master's Degrees" section under "Undergraduate Degrees and Programs" in the current Stanford Bulletin for additional information.

The coterminal Master of Science program follows the same program requirements as the Master of Science (Professional), except for the requirement to be employed in a corporate setting. The coterminal degree is only available to current Stanford undergraduates. Coterminal students are enrolled full-time and courses are taken on campus. Research projects are optional and the student must make arrangements with program faculty. Graduates of this program are prepared to contribute creatively to basic or applied projects in biomedical informatics.

DOCTOR OF PHILOSOPHY

The University's basic requirements for the doctorate (residence, dissertation, examination, and so on) are discussed in the "Graduate Degrees" section of the current Stanford Bulletin.

Individuals wishing to prepare themselves for careers as independent researchers in biomedical informatics, with applications experience in bioinformatics, clinical informatics, or imaging informatics, should apply for admission to the doctoral program. The following are additional requirements imposed by the Biomedical Informatics Interdisciplinary Committee:

  1. A student should plan and successfully complete a coherent program of study including the core curriculum, oral examination, and additional requirements for the master's program. In addition, doctoral candidates are expected to take at least two more advanced courses (see categories under item '2' of the master's program requirements). In the first year, two or three research rotations are strongly encouraged. The master's requirements, including the oral examination, should be completed by the end of the second year in the program (six quarters of study, excluding summers). Doctoral students are generally advanced to PhD candidacy after completing the oral examination. A student's academic adviser has primary responsibility for the adequacy of the program, which is regularly reviewed by the Graduate Study Committee of the Biomedical Informatics program.


  2. To remain in the PhD program, each student must attain a grade point average (GPA) as outlined above, and must pass a comprehensive exam covering introductory level graduate material in any curriculum category in which he or she fails to attain a GPA of 3.0. The student must fulfill these requirements and apply for admission to candidacy for the PhD by the end of six quarters of study (excluding summers). In addition, reasonable progress in the student's research activities is expected of all doctoral candidates.


  3. During the third year of training, generally in the Winter Quarter, each doctoral student is required to give a preproposal seminar that describes evolving research plans and allows program faculty to assure that the student is making good progress toward the definition of a doctoral dissertation topic. By the end of nine quarters (excluding summers), each student must orally present a thesis proposal to a dissertation committee that generally includes at least one member of the Graduate Study Committee of the Biomedical Informatics program. The committee determines whether the student's general knowledge of the field, and the details of the planned thesis, are sufficient to justify proceeding with the dissertation.


  4. As part of the training for the PhD, each student is required to be a teaching assistant for two courses approved by the BMI exec; one should be completed in the first two years of study.


  5. The most important requirement for the PhD degree is the dissertation. Prior to the oral dissertation proposal and defense, each student must secure the agreement of a member of the program faculty to act as dissertation adviser. The principal adviser need not be an active member of the Biomedical Informatics program faculty, but all committees should include at least one participating BMI faculty member.


  6. No oral examination is required upon completion of the dissertation. The oral defense of the dissertation proposal satisfies the University oral examination requirement.


  7. The student is expected to demonstrate an ability to present scholarly material orally and present his or her research in a lecture at a formal seminar.


  8. The student is expected to demonstrate an ability to present scholarly material in concise written form. Each student is required to write a paper suitable for publication, usually discussing his or her doctoral research project. This paper must be approved by the student's academic adviser as suitable for submission to a refereed journal before the doctoral degree is conferred.


  9. The dissertation must be accepted by a reading committee composed of the principal dissertation adviser, a member of the program faculty, and a third member chosen from anywhere within the University.

 

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