printer friendly pageBIOS 205: Introduction to R for Data Analysis
Autumn quarter enrollment limited to ADVANCE students; instructor consent required for enrollment. Topics include: basics of R (widely used, open-source programming and data analysis environment) programming language and data structures, reading/writing files, graphics tools for figure generation, basic statistical and regression operations, survey of relevant R library packages. Interactive format combining lectures and computer lab. For course and enrollment information, see
https://web.stanford.edu/~sbagley2/bios205/
Terms: Aut, Win, Spr
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Units: 1
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Grading: Medical Satisfactory/No Credit
Instructors:
Bagley, S. (PI)
BIOS 226: Introduction to Force Spectroscopy
Mini-course. Covers the fundamentals of major single-molecule manipulation methods (optical tweezers, magnetic tweezers, and atomic force microscopy), principles of force measurement signal and noise, and applications to studies of folding, binding, polymer elasticity, and structural transitions in proteins and nucleic acids. Intended for students with no previous exposure to single-molecule manipulation or for beginning practitioners. Lectures and discussion of current literature.
Terms: Spr
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Units: 1
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Grading: Letter or Credit/No Credit
Instructors:
Bryant, Z. (PI)
;
Ruijgrok, P. (TA)
BIOS 235: Metabolism and Metabolic Ecology: Microbes, Gut and Cancer
Preference to graduate students. Focuses on modern aspects of metabolism and metabolic biochemistry as it affects fitness and ecology of cells and organisms on a systems level. Students obtain a broad understanding of the governing principles and logic of metabolic pathways and their networks as well as an intuition of metabolism in context of natural selection and fitness acting on the cell or host. Emphasis is primarily on microorganisms and their habitats in nature and the human gut, but topics also include metabolism of cancer cells and of engineered microbes.
Terms: Spr
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Units: 2
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Grading: Medical Option (Med-Ltr-CR/NC)
Instructors:
Spormann, A. (PI)
BIOS 236: Developmental Biology in the Ocean: Comparative Embryology and Larval Development
Three-week course at Hopkins Marine Station. Focuses on the embryology and larval development of a broad range of marine invertebrate phyla. The goal of the course is to give students an appreciation of the range of developmental strategies and larval forms in the ocean and why this is critical for constructing hypotheses of EvoDevo and animal evolution. Includes observation and documentation of the development of embryos and larvae by scientific illustration and photo/video microscopy. Pre-requisite: Developmental Biology coursework and instructor consent.
Terms: Spr
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Units: 4
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Grading: Medical Option (Med-Ltr-CR/NC)
Instructors:
Lowe, C. (PI)
BIOS 254: DataLucence::Images
Increasingly, research in the biosciences involves data in digital formats and scientists spend a significant fraction of their time building and using software to harvest insight from digital data. A central goal of this course is to expose students to concepts adopted from computer science and data science regarding data management, data curation, and analytical workflows for analyzing digital data. We will focus on digital images since this image type is used in diverse sub-fields in the biosciences. The course will consist of a two-day workshop/lab¿SoftwareCarpentry¿and six DataLucence::Images+Hackathon class meetings.
Terms: Aut
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Units: 2
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Grading: Medical Option (Med-Ltr-CR/NC)
BIOS 256: Sculptural Data Illustrations
Mini-course. Students will use learn make and print 3D models of their data to use as a focal point when describing their project. We will teach the students how to use Autocad and Blender to process existing data sets and students are encouraged to bring their own data. We strive to make wearable models to enable instant mini-lectures any place and anytime.
Terms: Win, Spr
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Units: 1
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Grading: Medical Option (Med-Ltr-CR/NC)
Instructors:
Schneider, D. (PI)
BIOS 263: Applied Grant-Writing Skills for Fellowships
Graduate students in the Biosciences PhD Programs develop a fellowship proposal (e.g. NIH F31) focusing on required documents: 1-page specific aims as well as research and career development plans. Students establish a writing practice and learn fundamental grant writing skills through guided exercises, including in-class review and focused faculty feedback.
Terms: Spr
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Units: 2
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Repeatable for credit
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Grading: Medical Satisfactory/No Credit
BIOS 265: Introduction to Quantitative Reasoning in Biology
Mini-course. Focus on development of basic skills for quantitative reasoning in biology, including order-of-magnitude estimation and use of the broad spectrum of time scales to enable understanding. Primary examples include going from molecular size and energy scales to functions of single cells and going from mutational and selective processes acting on organisms to evolution of populations on laboratory global scales.
Terms: Spr
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Units: 2
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Grading: Medical Satisfactory/No Credit
Instructors:
Fisher, D. (PI)
BIOS 266: Mini Proposal Bootcamp
In an intensive 1-day format, students learn the fundamentals for writing competitive fellowships, i.e. NIH NRSA fellowships (F30, F31, F32). Topics include developing specific aims; outlining research and career development plans; and using the review criteria to inform writing. Students develop early drafts of the 1-page specific aims, NIH biosketch, and training plan, and receive feedback from instructor. Students are expected to be in the early stages of writing a fellowship proposal.
Terms: Spr
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Units: 1
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Grading: Medical Satisfactory/No Credit
Instructors:
Botham, C. (PI)
;
Talbot, W. (PI)
BIOS 268: Biology and Applications of CRISPR/Cas9: Genome Editing and Epigenome Modifications (GENE 268)
This course is designed to provide a broad overview of the biology and applications of the revolutionary CRISPR/Cas9 system, with detailed exploration of several areas: / / --Basic biology of the CRISPR/Cas9 system / --High-throughput screening using CRISPR/Cas9 / --Epigenetic modifications and transcriptional regulation using dCas9 / --Therapeutic applications of gene editing with CRISPR / --Disease modeling with CRISPR / --Ethical considerations of the use of CRISPR/Cas9 / / The course will be geared toward advanced undergraduates and graduate students, and will assume a basic background in molecular biology and genetics. The course will be lecture-based, with frequent opportunities for discussion and questions.
Terms: Spr
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Units: 1
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Grading: Medical Satisfactory/No Credit
Instructors:
Bassik, M. (PI)
;
Carette, J. (PI)
;
Cho, M. (PI)
;
Porteus, M. (PI)
;
Qi, S. (PI)
;
Winslow, M. (PI)
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