The widespread adoption of electronic health records (EHRs) has created a new source of big data namely, the record of routine clinical practice as a by-product of care. This graduate class will teach you how to use EHRs and other patient data to discover new clinical knowledge and improve healthcare. Upon completing this course, you should be able to: differentiate between and give examples of categories of research questions and the study designs used to address them, describe common healthcare data sources and their relative advantages and limitations, extract and transform various kinds of clinical data to create analysis-ready datasets, design and execute an analysis of a clinical dataset based on your familiarity with the workings, applicability, and limitations of common statistical methods, evaluate and criticize published research using your knowledge of 1-4 to generate new research ideas and separate hype from reality. 

Instructors: Shah, N.

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The course will focus on computational approaches to ensure that all data, code, and analyses can be captured in a reproducible workflow, to be confirmed and replicated by you in the future, by other members of your team, and by reviewers and other researchers. We will cover how to satisfy FAIR principles, version control, how to create a git repository, utilize Github and how to create a reproducible dataset. Prerequisites: Basic knowledge of R.

Instructors: Goodman, S.

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We will cover the philosophical framework of bio(medical)ethics and good scientific practice in daily modules. The itinerary includes the History of Bioethics, Formal Logic, Moral Philosophy (Virtue Ethics, Utilitarianism, Deontology, Feminist Ethics), Medical & Bioethics, Animal Welfare, Good Scientific Practice, and Science Ethics.

Instructors: Sudhof, T.; Thome, C.

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This 2-week mini-course will discuss pragmatic approaches to rodent utilization with the aim of empowering graduate students across multiple disciplines to maximize rodent-derived data and minimize the redundant use of animals in biomedical research. Topics will include an introduction to clinical models, practical aspects of rodent blood collection and interpretation, algorithmic approaches to tissue collection for research applications, and an introduction to rodent histopathology, immunohistochemistry, and immunofluorescence. Course instructors include board-certified laboratory animal medicine clinicians and comparative pathologists that are expert h these topics. This course is open to graduate students with or without prior rodent experience.

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How and why animals are used in biomedical science. Addresses human and animal health and how animal research has contributed to the treatment and cure of disease. Significant portions of this course are devoted to documenting the humane care and treatment of laboratory animals in research, including, but not limited to such topics as law and ethics, animal behavior, animal modeling, and the animal activist movement. Course topics will also include: history of animals in research, environmental enrichment for research animals, and research animals in the media. Includes hands-on workshops covering animal handling, aseptic rodent surgery, and mouse breeding.

Instructors: Albertelli, M. (PI)

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Emphasis is on providing introductory training and practical, hands-on research animal biomethodology. Topics include basic care and principles guiding the use of research animals, animal health and welfare, enrichment, basic mouse handling, rodent breeding, and the principles of rodent aseptic surgery and anesthesia. The objective of this course is to teach basic skills in animal handling, animal care, and biomethodological research techniques. Content delivered online and in-person.

Instructors: Huss, M. (PI)

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Focuses on husbandry, care, and diseases of major laboratory animal species (rodents, fish and amphibians, swine, sheep, rabbits, monkeys); regulatory and compliance, applied principles of animal modeling, and factors that influence animal research, animal behavior, and research reproducibility. The objective of this course is to provide students with an overview of the history of laboratory animal science, current industry standards and practices, and the fundamentals of laboratory animal diseases. Department consent is required for enrollment. May be repeated for credit. The course is virtual. Must attend 7 out of 10 seminars in the quarter for a satisfactory grade.

Instructor: Nagamine, C.

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So you've taken all these stats classes and learned a bunch of equations, but now you have to design and analyze your own experiments, and you're feeling lost and all those equations and classes really don't make sense. DON'T PANIC, we've all been there, and this is the class for you! Try learning these essential skills a different way - conceptually and hands-on without equations. Emphasis is on real-world experimental design and analysis in the life sciences, with particular focus on modern techniques that maximize power and minimize sample size, and avoiding common errors contributing to false discovery and the reproducibility crisis. This is a flipped-classroom. Class time is devoted to discussion of assigned reading (primarily Grafen & Hails 2002 "Modern statistics for the life sciences"), hands on guided work-through of example data sets, and developing analyses for the students' own research data. The objective is to provide students with a foundational conceptual understanding of biostatistics, particularly as applied to the design and planning of animal-based research projects.

Instructors: Garner, J. (PI)

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Research laboratory and clinical service (pathology, diagnostic laboratory, surgery, husbandry, anesthesiology, aquatics, facility business and management, etc.), quarterly rotations for students enrolled in the Master's of Laboratory Animal Science program. The objective of this course is to provide students with hands on experience in research laboratories using animal models and to provide experience working in the daily operations of a large, veterinary service center. Fulfills the practicum and research requirements of MLAS students.

Instructors: Albertelli, M. ; Bentzel, D. ; Casey, K. ; Darian-Smith, C. ; Felt, S.; Garner, J.; Green, S.; Hestrin, S. ; Huss, M.; Nagamine, C.; Pacharinsak, C. ; Parker, K. ; Vilches-Moure, J.

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Focus is on career development for graduate students and trainees enrolled in a trainee program in the Department of Comparative Medicine. Seminar topics include career pathways in laboratory animal science, resume preparation, manuscript preparation and authorship, life in academics, life in industry and biopharma, regulatory agencies, veterinary and medical school. Speakers include faculty, speakers from industry and pharmaceutical companies, veterinary school and medical school graduates, regulatory and compliance professionals, research scientists, and animal research program/laboratory managers. Students may choose to shadow veterinary clinical faculty or rotate through basic science laboratory, by special arrangement. The objective is to introduce students to the multiple career pathways available to individuals with advanced training in laboratory animal science. May be taken up to six quarters.

Instructor: Green, S.

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Prerequisite: consent of instructor. (Staff)

Terms: Aut, Win, Spr, Sum | Units: 1-18 | Repeatable for credit

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Open to graduate, medical, and undergraduate students. Appraisal of the quality and credibility of research findings; evaluation of sources of bias. Meta-analysis as a quantitative (statistical) method for combining results of independent studies. Examples from medicine, epidemiology, genomics, ecology, social/behavioral sciences, education. Collaborative analyses. Project involving generation of a meta-research project or reworking and evaluation of an existing published meta-analysis. Prerequisite: knowledge of basic statistics.

Instructors: Ioannidis, J.

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The course will consist of readings and discussion of foundational papers and book sections in the domains of statistical and scientific inference. Topics to be covered include philosophy of science, interpretations of probability, Bayesian and frequentist approaches to statistical inference and current controversies about the proper use of p-values and research reproducibility.

Instructor: Goodman, S.

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This discussion focused Ethics, Science, and Society interactive mini-course will engage Immunology graduate students, postdoctoral fellows, and faculty in learning and conversations on topics in responsible research (including animal subjects, authorship, collaboration, conflicts of interest, data management, human subjects, mentor-mentee relationships, peer review, publication, research misconduct, and social responsibility) and diversity in science, informed by readings, case studies, individual reflections, and more. Some of the driving themes in this course include: what it means to do research well and how to and not to achieve this, why doing research well and with integrity is important, and who are researchers currently and who should they be.

Instructor: Martinez, O.

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This course presents a survey of the historical and current status of this rapidly developing specialty. In brief, animal law encompasses all areas of the law in which the nature -- legal, social or biological -- of nonhuman animals is an important factor. It is an objective and logical specialization of a challenging area -- one with a growing number of cases and laws, increasing public and practical interest, and significantly different historical, legal and philosophical foundations than most other courses. Topics covered include animal cruelty, animals as property, tort claims regarding animals, legal issues involving farm animals and animals in entertainment, and federal statutes regarding certain groups of animals. The Animal Law course has been described as intellectually stimulating and ethically challenging, and synthesizes a wide range of legal concepts, and the course materials apply traditional ideas to legal concepts associated with animals in new ways. Students have called it a great bar review class, because concepts from many areas of law are covered with respect to their application to animals and their interests. More and more firms, large and small, are providing pro bono (and paying) work in the animal law area, as the field gains momentum and reputability in the legal community. Mr. Wagman is a lawyer in San Francisco, with a full-time animal law practice, representing organizations and individuals in a wide range of cases. He is one of the authors of the Animal Law casebook, two other animal legal texts, and has been practicing animal law for most of his 30-year career. His practice includes litigation, consultation, legislative work, and extensive writing and lecturing on various animal law topics. The class includes regular updates on his current cases, which for this semester includes a case that will be argued in the U.S. Supreme Court in the October 2022 term. He also regularly provides real-life experiences from the front lines of the field. Special Instructions: Students have the option to write an independent research paper in lieu of the final exam with consent of instructor.

Instructor: Wagman, B.

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This course introduces standard and acceptable practices in the life sciences, with an emphasis on responsibilities in research activities such as record keeping, data treatment, authorship, peer review, mentoring and participation in research that engages human or animal subjects. Conflicts of interest, ownership of date and other intellectual property and potential problems stemming from use of data from human genetics or stem cell experiments are examples of additional topics for discussion. Open to upper-level undergraduate students, medical students, graduate students and M.D. and Ph.D. postdoctoral fellows. This course is required for trainees supported by the NIH Pediatric Nonmalignant Hematology and Stem Cell Biology training program.

Instructor: Sakamoto, K.

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