Biomedical Informatics

Distance Education Programs

Overview

Biomedical informatics is an interdisciplinary fieldthat combines ideas from computer science andquantitative disciplines to solve challenging prob-lems in biology and medicine.

Stanford’s program is particularly strong in meth-ods development, drawing heavily on quantita-tive and computational approaches. Note thatour prerequisites include mathematics, probabilityand statistics, and computer programming. Manyother programs are more applied in nature.

Our distance education program offers individ-ual courses, a three-course certificate, and a dis-tance education masters degree. Students receivecourse content and interact via the Stanford Cen-ter for Professional Development (SCPD, http:

//scpd.stanford.edu). Students enrolled in theMS degree program are also allowed to attendclass on campus if they desire.

Certificate in Biomedical In-formatics

Prerequisites

The following are required for entry into the Cer-tificate Program. Note that these prerequisitecourses do not count towards the Certificate, evenif taken at Stanford.

1. A bachelor’s degree with a 3.0 (B) gradepoint average or better.

2. One year of computer programming or soft-ware engineering coursework or equivalentexperience. We recommend that studentstake the equivalent of Stanford’s CS 106Aand 106B prior to entering the CertificateProgram.

3. At least some college biology, preferably oneyear.

4. One year of calculus is required for someclasses, and is strongly recommended so that

a student is able to take any of the certificatecourses.

5. Classwork in probability and statistics is aprerequisite for some classes.

Tuition

The cost of the certificate depends on the numberof units taken. The current tuition is $1,200 perunit. Details are at http://scpd.stanford.edu/admissions/tuition-fees.

How to Apply

You apply to take individual courses or coursesfor the Certificate programs through SCPD (http://scpd.stanford.edu).

Certificate courses

Three courses are required for the Biomedical In-formatics Certificate. These courses, which are de-scribed in detail later in this brochure, are chosenfrom the following list:

• BIOMEDIN 210: Modeling Biomedical

Systems: Ontology, Terminology, Prob-lem Solving

• BIOMEDIN 214: Representations and Al-gorithms for Computational Molecular

Biology

• BIOMEDIN 215: Data Driven Medicine

• BIOMEDIN 217: Translational Bioinfor-matics

• BIOMEDIN 260: Computational Methods

for Biomedical Image Analysis

Masters Degree Program

Stanford BMI has a distance education MS pro-gram. It is offered through SCPD under the Hon-ors Cooperative Program, or Professional Science

Masters model. It is designed for employed pro-fessionals working in the general area of biomedi-cal informatics, who want further training leadingto a degree. The HCP MS degree is fully equiv-alent to a regular Stanford MS degree. You canlearn more about the HCP program and employ-ment requirements at the SCPD website.

Prerequisites

The prerequisites are shown, along with the equiv-alent Stanford courses. Note that these are theminimum requirements needed to be able to be-gin graduate-level coursework in our program andthat many applicants exceed them.

1. One year of calculus. Further coursework inmultivariate calculus (MATH 51 and MATH52) is strongly recommended.

2. Coursework in probability and statistics(STATS 116), and linear algebra (MATH 104

or MATH 113).3. One year of computer program-

ming/computer science coursework (CS106A and CS 106B). The focus should befundamentals of computer science and soft-ware engineering principles, including ab-straction, modularity, and object-orientedprogramming, not merely the syntax of aprogramming language, scripting, or webprogramming.

4. One year of college biology at the level re-quired of biology majors (BIO 41, BIO 42,and corresponding laboratory BIO 44X).

Tuition

Stanford requires 45 units for an MS degree. Thecurrent rate set by SCPD is $1,400 per unit, sothe total would be $63,000. Details are at http://scpd.stanford.edu/admissions/tuition-fees.

How to Apply

You apply to the MS program through BMI athttp://bmi.stanford.edu/prospective-students/.

Curriculum

The course requirements for the MS degree arelisted at http://exploredegrees.stanford.edu/schoolofmedicine/biomedicalinformatics/

#masterstext. In summary, the required course-work is:

1. Core Biomedical Informatics (15 or moreunits). Students complete the core:BIOMEDIN 212, and four courses cho-sen from BIOMEDIN 210, BIOMEDIN214, BIOMEDIN 215, BIOMEDIN 217, andBIOMEDIN 260.

2. Computer Science, Statistics, Mathematicsand Engineering (18 units). Students are ex-pected to create a program of study witha mixture of graduate-level courses in com-puter science, statistics or other technicalinformatics-related disciplines that allowsthem to achieve in-depth mastery of theseareas. CS 161 Design and Analysis of Algo-rithms, and STATS 200 Introduction to Sta-tistical Inference are required. These twocourses, or some of their prerequisites, maynot be available through SCPD. You shoulddesign a course plan with next best alter-natives: these may include similar coursesat Stanford, or courses at other institutions(outside courses would not count towardsthe required 45 units). Alternatively, youcould take the courses on-campus if you livenearby.

3. Social and Ethical Issues (4 units)

4. Unrestricted Electives at the graduate levelto complete the required 45 units.

Transfer Credits

Stanford does not allow transferring credits fromoutside institutions towards the MS degree. How-ever, up to 15 units of Stanford coursework, eitherindividual courses, or those taken for the certifi-cates, can be counted towards the MS degree.

Course List

The follow is a list of the courses for the certifi-cate and the MS core. A complete list of Stanford

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courses is at: http://explorecourses.stanford.edu.

BIOMEDIN 210. Modeling Biomedical Systems:Ontology, Terminology, Problem Solving. 3

units, Winter. Methods for modeling biomedicalsystems and for making those models explicit inthe context of building software systems. Empha-sis is on intelligent systems for decision supportand Semantic Web applications. Topics: knowl-edge representation, controlled terminologies, on-tologies, reusable problem solvers, and knowledgeacquisition. Prerequisites: CS106A, basic familiar-ity with biology.

BIOMEDIN 212. Introduction to Biomedical

Informatics Research Methodology. 3 units,Spring, available to HCP students on experimental ba-sis. Hands-on software building. Student teamsconceive, design, specify, implement, evaluate,and report on a software project in the domain ofbiomedicine. Creating written proposals, peer re-view, providing status reports, and preparing finalreports. Guest lectures from professional biomed-ical informatics systems builders on issues relatedto the process of project management. Softwareengineering basics. Prerequisites: BIOMEDIN 210

or 211 or 214 or 217. Preference to BMI graduatestudents. Consent of instructor required.

BIOMEDIN 214. Representations and Algo-rithms for Computational Molecular Biol-ogy. 3–4 units, Autumn. Topics: introductionto bioinformatics and computational biology, al-gorithms for alignment of biological sequencesand structures, computing with strings, phylo-genetic tree construction, hidden Markov mod-els, Gibbs Sampling, basic structural computationson proteins, protein structure prediction, proteinthreading techniques, homology modeling, molec-ular dynamics and energy minimization, statisticalanalysis of 3D biological data, integration of datasources, knowledge representation and controlledterminologies for molecular biology, microarrayanalysis, machine learning (clustering and classifi-cation), and natural language text processing. Pre-requisite: CS 106B; recommended: CS161; consentof instructor for 3 units.

BIOMEDIN 215. Data Driven Medicine. 3

units, Autumn. With the spread of electronichealth records and increasingly low cost assaysfor patient molecular data, powerful data reposito-ries with tremendous potential for biomedical re-search, clinical care and personalized medicine are

being built. But these databases are large and dif-ficult for any one specialist to analyze. To find thehidden associations within the full set of data, weintroduce methods for data-mining at the internetscale, the handling of large-scale electronic medi-cal records data for machine learning, methods innatural language processing and text-mining ap-plied to medical records, methods for using on-tologies for the annotation and indexing of un-structured content as well as semantic web tech-nologies. Prerequisites: CS 106A; STATS 216. Rec-ommended: one of CS 246, STATS 305, or CS 229

BIOMEDIN 217. Translational Bioinformat-ics. 4 units, Winter. Analytic, storage, and in-terpretive methods to optimize the transformationof genetic, genomic, and biological data into diag-nostics and therapeutics for medicine. Topics: ac-cess and utility of publicly available data sources;types of genome-scale measurements in molecu-lar biology and genomic medicine; analysis of mi-croarray data; analysis of polymorphisms, pro-teomics, and protein interactions; linking genome-scale data to clinical data and phenotypes; andnew questions in biomedicine using bioinformat-ics. Case studies. Prerequisites: programmingability at the level of CS 106A and familiarity withstatistics and biology.

BIOMEDIN 224: Principles of Pharmacoge-nomics. 3 units, Spring. This course is an intro-duction to pharmacogenomics, including the rele-vant pharmacology, genomics, experimental meth-ods (sequencing, expression, genotyping), dataanalysis methods and bioinformatics. The coursereviews key gene classes (e.g., cytochromes, trans-porters) and key drugs (e.g., warfarin, clopidogrel,statins, cancer drugs) in the field. Resources forpharmacogenomics (e.g., PharmGKB, Drugbank,NCBI resources) are reviewed, as well as issuesimplementing pharmacogenomics testing in theclinical setting. Reading of key papers, includingstudent presentations of this work; problem sets;final project selected with approval of instructor.Prerequisites: two of BIO 41, 42, 43, 44X, 44Y orconsent of instructor.

BIOMEDIN 260. Computational Methods for

Biomedical Image Analysis and Interpreta-tion. 3–4 units, Spring. The latest biological andmedical imaging modalities and their applicationsin research and medicine. Focus is on computa-tional analytic and interpretive approaches to op-timize extraction and use of biological and clin-ical imaging data for diagnostic and therapeutic

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translational medical applications. Topics includemajor image databases, fundamental methods inimage processing and quantitative extraction ofimage features, structured recording of image in-formation including semantic features and ontolo-gies, indexing, search and content-based image re-trieval. Case studies include linking image data togenomic, phenotypic and clinical data, develop-ing representations of image phenotypes for use

in medical decision support and research applica-tions and the role that biomedical imaging infor-matics plays in new questions in biomedical sci-ence. Includes a project. Enrollment for 3 units re-quires instructor consent. Prerequisites: program-ming ability at the level of CS 106A, familiaritywith statistics, basic biology. Knowledge of Mat-lab or Python highly recommended.

Contact Information

For questions about courses and degrees require-ments, review the relevant sections of http://

bmi.stanford.edu, and send remaining questionsvia email to bmi-contact@lists.stanford.edu.

For questions about receiving the course videoover the Internet, employment requirements, andtuition, please review the relevant sections ofhttp://scpd.stanford.edu, and send remain-ing questions to SCPD at: scpd-gradstudents@

stanford.edu.

Version of Jan 29, 2018

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