170.03

Medical Imaging Informatics

(2 units)

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Winter

Instructor(s):K. Young, N. Schuff Prerequisite(s): Previous courses in Principles of Magnetic Resonance or Magnetic Resonance Spectroscopy or consent of istructor.

Restrictions:None Activities: Lecture: 2 hours

This course will focus on teaching modern techniques for the analysis of multi-parametric medical imaging data, including structural, functional, and spectroscopic imaging. The objective is to introduce students to modern methods for processing and analysis of large volumes of heterogeneous data with a specific focus on MRI data. (RADIOLOGY)

202

Decision Making in the Health Sciences

(3 units)

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Winter

Instructor(s):D. Hudson, M. Cohen Prerequisite(s): At least one programming class, mathematical background through simple differential equations. Consent of instructor.

Activities: Lecture: 3 hours

Introduction to principles and techniques for computer-assisted decision making in the health sciences. Topics include rules-based systems, neural networks and other statistical approaches to decision support. (BIO MD INF)

203

Biocomputing Algorithms

(3 units)

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Winter

Instructor(s):A. Jain Prerequisite(s): Students are expected to have programming competence in a language such as Python, C, C++, or Fortran. Students should also posses a basic knowledge of statistics (undergrad. level).

Restrictions:For all iPQB students and Bioengineering students. Others require instructor approval. Activities: Lecture: 2 hours, Laboratory: 1 hours, Project: 0.5 - 1 hours, Independent Study: 0.5 hours

Introduction to computational issues and methods used in the field of bioinformatics and computational biology. This course emphasizes the implementation, analysis, and validation of methods. It is about attacking computational problems in biology, not expert use of existing tools. Areas addressed include analytical thinking, problem decomposition, and algorithm design and implementation. Assignments will focus on the design and implementation of key bioinformatics algorithms. (BIO MD INF)

206

Introduction to Bioinformatics

(3 units)

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Fall

Instructor(s):P. Babbitt, T. Kortemme, A. Sali Prerequisite(s): Upper division course work in biological sciences including knowledge of proteins and protein structure, computer literacy.

Restrictions:None. Activities: Lecture: 2 hours, Seminar: 3 hours

Broad survey of bioinformatics with accompanying assignments. Topics covered include genomics, database searching, family/super-family analysis, structural genomics, complex systems, genetic circuits, and protein-protein interactions. (BIO THERAP)

207

Statistics

(2.0 units)

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Winter

Instructor(s):J. Song Prerequisite(s): Linear algebra and calculus.

Restrictions:None Activities: Lecture: 15 hours, Independent Study: 15 hours

This course will introduce basic probability theory and fundamental ideas in statistics. It will cover probability distributions, random variables, Monte Carlo techniques, Markov processes, parametric and non-parametric statistical tests, and linear models. Examples will be drawn from genomics. Familiarity with linear algebra and calculus will be assumed. (PHARM CHEM)

209

Statistical Analysis of Microarray Data

(1 units)

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Spring

Instructor(s):M. Segal

Activities: Lecture: 1 hours

This course offers students a series of weekly lectures detailing methods for the analysis of microarray data. After reviewing microarray technology, a range of statistical techniques corresponding to frequently encountered research questions and study design are illustrated and evaluated. Tools for effecting such analyses are also described. (PHARM CHEM)

219

Special Topics in Bioinformatics

(3 units)

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Spring

Instructor(s):Staff Prerequisite(s): None.

Restrictions:Priority given to first-year graduate students. Activities: Lecture: 1 hours, Conference: 2 hours, Independent Study: 3 hours

Each course offering will focus on the literature of a current important area of Bioinformatics. Students will be expected to read assigned papers critically before class and to present and discuss papers in class. Students will also be expected to write and present a brief research proposal based upon their reading. Topics in Molecular, Cellular, developmental, systems, and computation biology will be covered in separate course offerings. (BIO THERAP)

220

Informatics Seminar

(1 units)

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Fall, Winter, Spring

Instructor(s):T. Ferrin

Activities: Seminar: 1 hours

Presentation and discussion of bioinformatics and medical informatics research topics. (BIO MD INF)

221

Informatics Rotation

(1 - 8 units)

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Fall, Winter, Spring, Summer

Instructor(s):Staff

Activities: Laboratory: 3 - 24 hours

An introduction to the specific research currently underway within a faculty member's laboratory. (BIO MD INF)

222

Student Informatics Seminar

(1 units)

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Fall, Winter, Spring

Instructor(s):T. Ferrin

Activities: Seminar: 2 hours, Library: 1 hours

This course gives students the opportunity to develop and polish their presentation and research skills. All second year and above BMI students present their research to other students, postdocs and faculty. Their presentations are critically evaluated and they are provided with constructive feedback regarding their discussion topic and presentation skills. (BIO MD INF)

223

Critical Topics in Biomedical Informatics

(1 units)

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Fall, Winter, Spring

Instructor(s):T. Ferrin Prerequisite(s): None.

Restrictions:None. Activities: Seminar: 3 hours

Critical review of published scientific papers from scholarly journals, including comprehension, analysis and evaluation of published scientific data. (BIO THERAP)

224

Graduate Research Opportunities Seminar

(1 units)

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Fall, Winter

Instructor(s):T. Ferrin

Restrictions:First year BMI students. Activities: Seminar: 1 hours

This course offers 1st year students a series of weekley presentations of the research interests of the BMI basic science faculty. The purpose is to acquaint new graduate students with research projects and opportunities in faculty labs. The course is modeled after PSPG 225 A&B. (BIO MD INF)

225

Research Project

(1 - 8 units)

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Fall, Winter, Spring, Summer

Instructor(s):Staff

Restrictions:MS students only. Activities: Project: 3 - 24 hours

A significant, planned, indepndent research project in collaboration with research advisor, and designed to make a practical contribution to the field of informatics. Final report fulfills requirement for MS degree. (BIO MD INF)

250

Research

(1 - 8 units)

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Fall, Winter, Spring, Summer

Instructor(s):Staff

Activities: Project: 3 - 24 hours

For PhD students working with research advisor in preparation for oral qualifying exam. (BIO MD INF)

280

Scientific Software Development

(1 units)

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Spring

Instructor(s):T. Ferrin, C. Huang Prerequisite(s): None.

Restrictions:None. Activities: Lecture: 1 hours

This course is an intensive introduction to basic software development practices for scientists and engineers. The goal is to provide scientists with the skills needed to create more reliable and maintainable programs while reducing the time spent on programming by 20-25%. (BIO MD INF)

283

Information Technology and Organizational Change

(2 - 3 units)

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Spring

Instructor(s):R. Miller Prerequisite(s): Consent of instructor.

Activities: Laboratory: 0 - 3 hours, Seminar: 2 hours

Course examines information technology (IT) in health care organizations, with a focus on electronic medical records. Course covers potential for IT to improve quality; economics of IT in health care; main theories of diffusion of innovations; alternative theories of the interrelationship between IT, behavior, process change, and organizational changes; and alternative policy approaches to hasten IT adoption in health care. Cross-listed with Sociology. (BIO MD INF)

299

Dissertation

(0 units)

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Fall, Winter, Spring, Summer

Instructor(s):Staff Prerequisite(s): Advancement to candidacy.

Restrictions:BMI students only.

For students advanced to candidacy working on their dissertation. (BIO MD INF)