BIOS 200:
Foundations in Experimental Biology
This course is divided into two 3-week cycles. During the first cycle, students will be developing a 2-page original research proposal, which may be used for NSF or other fellowship applications. In the second cycle, students will work in small teams and will be mentored by faculty to develop an original research project for oral presentation. Skills emphasized include: 1) reading for breadth and depth; 2) developing compelling, creative arguments; 3) communicating with the spoken and written word; 4) working in teams. Important features of the course include peer assessment, interactive joint classes, and substantial face-to-face discussion with faculty drawn from across the Biosciences programs. Shortened autumn quarter class; class meets during weeks 1 through 8 of the quarter.
Terms: Aut
| Units: 5
BIOS 201:
Next Generation Sequencing and Applications
Usher in the golden age of biological discovery with next generation sequencing (NGS) through its wide spectrum of applications. Modules include general introduction of Next Generation Sequencing (NGS) technologies, applications of these sequencing technologies, caveats and comparisons with previous approaches, analysis and interpretation of sequencing data, principles of tools and resources and practical ways to utilize them, and features and pitfalls. Prerequisite: background in molecular biology.
Terms: Win
| Units: 2
BIOS 202:
Hippocampal Field Potentials, an Introduction to CNS in Vitro Electrophysiology
Enrollment limited to graduate students in the School of Medicine; undergraduates may enroll with instructor consent. Introduces students to theory and practice of in vitro CNS electrophysiology. Lectures cover basic electrical and electrode theory, hippocampal anatomy, interpretation of these potentials, common pitfalls and misinterpretations, design of experiments using field potentials and other related topics. Practicum is hands on training in obtaining, recording and interpreting field potentials from in vitro hippocampal slices. Students develop skills in data collection, analysis and evaluation, art and design of electrophysiological studies of the brain.
Last offered: Winter 2013
| Units: 1-3
BIOS 203:
Introduction to Atomistic Simulations for Biochemical Applications
Theory and application of atomistic simulations needed to model and understand systems of biological relevance (proteins, DNA, small molecule therapeutic drug properties) for beginners. Topics: molecular interactions and classical force fields, first principles energy approaches, molecular dynamics, rare event and transition-state finding techniques, protein folding, and solvation methods. Hands-on tutorials based on key topics in biochemical simulation that use variety of state-of-the-art software packages on both standard and new, advanced graphical processing unit hardware for simulation and analysis ofnnbiochemical properties. Prerequisites: Some knowledge of quantum mechanics, biochemistry, and shell scripting (BASH or python) preferred.
Last offered: Winter 2013
| Units: 3
BIOS 204:
Practical Tutorial on the Modeling of Signal Transduction Motifs
Basics of ordinary differential equation modeling of signal transduction motifs, small circuits of regulatory proteins and genes that serve as building blocks of complex regulatory circuits. Morning session covers numerical modeling experiments. Afternoon session explores theory underpinning that day's modeling session. Modeling done using Mathematica, Standard Edition provided to enrolled students.
Terms: Spr
| Units: 3
BIOS 205:
Introduction to R
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 http://bios205.stanford.edu.
Terms: Aut, Win, Spr
| Units: 1
BIOS 206:
Stem Cells and Regeneration: Transitioning from Basic Research to Clinical Therapies
Presents emerging therapies based on stem cell by the scientists leading these pioneering efforts, including academic and industry-based groups. Provides hands-on instruction in laboratory methods valuable in development of stem cell therapies.
Last offered: Winter 2014
| Units: 1-2
BIOS 207:
Interdisciplinary Approaches to Biochemistry: Single Molecule Biophysics to Clinical Outcomes
Interdisciplinary analysis from basic biochemistry and biophysics to clinical outcomes of disease states and potential therapeutic interventions. Focus on cardiac system. Single molecule biophysics and classical enzyme kinetics and use of induced pluripotent stem (iPS) cells and single cell studies lay foundation for discussions of effects of cardiomyopathy mutations on heart function. Analytical approaches discussed include genetic analysis, reconstitution of functional assemblies, x-ray diffraction, 3D reconstruction of electron microscope images, spectroscopic methods, computational approaches, single molecule biophysics, use of induced pluripotent stem cells in research.
Last offered: Winter 2013
| Units: 1
BIOS 208:
Computational Macromolecule Structure Modeling
Concepts, workflow, and methodology of protein structure modeling presented through short lectures followed by hands-on exercises with the Rosetta software package. Several problem types demonstrate how to formulate and test well-defined hypotheses, in addition to the design and engineering of structure, function, and interactions.
Last offered: Spring 2015
| Units: 2
BIOS 209:
Practical Protein NMR Structure Determination
Work toward solving a high-resolution 3D structure from unprocessed NMR data acquired on a small well-characterized protein. Short lectures followed by hands-on computer exercises demonstrate best practices for data processing, spectra interpretation, and structure calculation with attention to troubleshooting and validation methods. Students should be familiar with fundamental concepts of protein structure and NMR spectroscopy and comfortable with the command-line environment. Prerequisite: SBIO242/BIOPHYS 242 strongly recommended, but not required.
Last offered: Winter 2014
| Units: 2
BIOS 210:
Axonal Transport and Neurodegenerative Diseases
Introduction to mechanisms underlying axonal transport, significance of proper regulation in maintaining neuronal activities, and its implication in disease pathology. Lab section: visualize axonal transport of various axonal organelles such as mitochondria, synaptic vesicles and dense core vesicles in live cells and tissues.
Last offered: Spring 2016
| Units: 1
BIOS 211:
Histology for Biosciences
Fundamentals of tissue organization as seen by light microscopy. Includes: epithelium, connective tissue, muscle, bone, cartilage, blood cells, nerve, and quick overview of several major organs. Each session has interactive 30 minutenpresentation followed by 1.5 hours viewing glass histology slides using individual microscopes and a multi-headed microscope. Slide sessions interspersed with interactive exercises to stimulate discussions. Supporting materials include select readings from histology atlas, electron micrographs, and virtual (whole-slide) images provided online.
Last offered: Spring 2016
| Units: 1
BIOS 213:
Scientific Illustration and Animation
Techniques of presenting big picture ideas and detailed experiments as simple cartoons. Mixed lecture/lab course culminates with students producing figures and animations for an introduction/conclusion of a research presentation. Covers basic design principles to help produce figures useful for broad and focused audiences. Includes static illustrations, Flash style, and stop motion animation.
Last offered: Spring 2015
| Units: 1
BIOS 214:
Molecules & Math
Introduction to molecular systems and their behavior as well as fundamental mathematical and computational tools for modeling molecular systems. Application of tools to critical medical areas: modeling of cardiovascular physiology; simulation of protein interactions; modeling of cellular differentiation; extraction of useful information from anatomic, functional and molecular images. Weekly lectures, group discussions, and individual project work.
Last offered: Spring 2013
| Units: 1
BIOS 215:
Transplantation Immunology and Tolerance
Extensive literature review of experimental strategies to promote tolerance, including limitations involved in translating tolerance-promoting strategies to the clinic and targets of Immunosuppression. State of art approaches and limitations of current approaches. Discussions with prominent scientists and clinicians in field of transplantation. Student presentations on novel concepts and approaches in basic science, translational and clinical transplant.
Last offered: Winter 2013
| Units: 2
BIOS 216:
Structural Biology and Vaccine Design
Structural biology is playing an increasing role in the development and analysis of vaccines and deepening understanding of challenging vaccine targets. Structural studies of target antigens have allowed mapping of neutralizing antibody epitopes and antigenic variation. Studies of antibody:antigen complexes have clarified how rare antibodies can confer broad neutralization to highly variant viruses, such as influenza virus and HIV. Course explores current structure-based efforts to improve vaccines to highly potent neutralizing epitopes, utilizing protein fragments, carbohydrate engineering and epitope scaffolding. Research from current literature on viruses including HIV, influenza virus, RSV and others examined.
Last offered: Spring 2013
| Units: 1
BIOS 217:
The Ultimate Face Book: Understanding Normal and Abnormal Craniofacial Development
How the face is assembled during embryonic development to gain insights into facial birth defects and new "regenerative medicine" approaches to reconstruct the face following disease or injury. Learn how "a man finds room in the few square inches of the face for the traits of all his ancestors; for the expression of all his history, and his wants."
Last offered: Winter 2013
| Units: 1
BIOS 218:
Molecular basis of membrane traffic
Transport of proteins through the secretory and endocytic pathways is essential for life; dysregulation causes disease and pathogens hijack these pathways to their best advantage. 5 international experts present didactic lectures and engage with students. Topics include: history of genetic and biochemical experiments to identify key components; reconstitution approaches; coated vesicle formation and cargo selection; control of membrane traffic by Rab GTPases; siRNA screens; high throughput microscopy analysis and systems biology approaches. Students devise and present research proposals based on the research of the guest speakers.
Last offered: Winter 2015
| Units: 2
BIOS 219:
Human Gene Regulation: Genomic Thinking and Genomic Tools for Experimentalists
Focused look at the promoter/enhancer and related landscape of the human genome. Genomics and epigenomics of human gene regulation - truth, myths and mysteries. Genomic tools for the interpretation of vertebrate gene regulation experiments and predictions, and the insights behind them. Genomic thinking: purity vs. comprehensiveness, genome-wide vs. single locus. Prerequisites: undergraduate Biology or equivalent. Programming skills not required or taught.
Last offered: Spring 2014
| Units: 1
BIOS 220:
Adventures in the Human Virosphere
Structure and function of viruses focusing on viruses that infect humans. Explore the interaction of humans and viruses from diverse perspectives: historical, cultural, political, demographic, organismal, molecular biological, biochemical, immunological, taxonomic. Emphasis on general principles of biology and matters of decision-making and policy. Selected case studies illustrate course material. Full-time immersive format of lectures, discussions, videos and model building. Recommended for non-virology students.
Last offered: Summer 2014
| Units: 3
BIOS 221:
Modern Statistics for Modern Biology (STATS 366)
Application based course in nonparametric statistics. Modern toolbox of visualization and statistical methods for the analysis of data, examples drawn from immunology, microbiology, cancer research and ecology. Methods covered include multivariate methods (PCA and extensions), sparse representations (trees, networks, contingency tables) as well as nonparametric testing (Bootstrap, permutation and Monte Carlo methods). Hands on, use R and cover many Bioconductor packages. Prerequisite: Minimal familiarity with computers. Instructor consent. Cross-listed as STATS 366.
Terms: Sum
| Units: 3
BIOS 222:
Authentic Courage for Constructive Change: Skills and Practice for Leadership
Explores concepts in decision making and constructive conflict as a mechanism for desired change via purposeful actions. Students assess personal conflict comfort zones and use case studies and class activities to develop skills with authenticity, active and intentional decision making, and other related topics.
Last offered: Spring 2015
| Units: 1
BIOS 223:
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.
Last offered: Winter 2016
| Units: 2
BIOS 224:
Big Topics in Stem Cell Ethics
Mini-course. Focuses on framing the major ethical issues, legal issues, normative ethical guidelines and oversight in stem cell research. Includes discussion of religious and ethical debates around the moral status of the human embryo.
Last offered: Winter 2014
| Units: 2
BIOS 225:
Diversity and Inclusion in Science
Introduction to the social science literature on factors contributing to gender disparities in the scientific workplace (e.g. implicit bias and stereotype threat). Discussions focus on steps that individuals and institutions can take to promote the advancement of women and other underrepresented groups in science, and thus promote the advancement of science.
Terms: Win
| Units: 1
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, 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.
Last offered: Spring 2014
| Units: 1
BIOS 227:
Mass Spectrometry and Proteomics: Opening the Black Box
Focus on designing and analyzing effective proteomics experiments using mass spectrometry and critically evaluating published mass spectrometry-based studies and datasets. Introduces students to the instrumentation, experimental strategies, and computational methods used for identifying and quantifying proteins and protein post-translational modifications using mass spectrometry. Topics include comparative evaluation of mass spectrometer instrument configurations, tandem mass spectrum interpretation, relative and absolute quantitation, and proteome-scale data set analysis. Laboratory time will focus on sample preparation methods, real-time data acquisition, and data analysis software and techniques.
Terms: Spr
| Units: 2
BIOS 228:
Understanding Chemistry in Biology and Biological Experiments
Chemical transformations are central to biology and function and chemical methods provide some of the most powerful tools for everyday experimental biology. Focuses on the concepts and principles underlying biological chemical transformations, allowing students to generalize and understand cell metabolism and regulation. Topics include basic principles and procedures to evaluate and utilize in practice chemical approaches in biological experiments. In-class problems and evaluation of literature. Three-week mini-course.
Last offered: Spring 2014
| Units: 2
BIOS 229:
Drug Discovery and Development Project Simulation
Two-day short course. Focus is on the progression of a drug discovery project from target identification through pre-clinical research, early and late clinical development, and registration with the health authorities. Presented by Novartis. Enrollment limited to postdoctoral students and graduate students with research experience.
Last offered: Summer 2016
| Units: 2
BIOS 230:
Biomedical Data Analysis in MATLAB
Focuses on empowering biomedical scientists and engineers with MATLAB tools that are directly useful in their research. Topics include linear- and non-linear-parameter estimation, ordinary- and partial-differential equations, Simulink, GUI design and image processing. Weekly hands-on tutorials accompany lectures and help students code more efficiently and elegantly. Weekly problems sets use MATLAB to interrogate a biomedical phenomenon. Pre-requisites: permission of instructor required.
Last offered: Spring 2015
| Units: 2
BIOS 231:
Neuroimaging Genomics
Preference to graduate students and medical students. Emphasis is on introducing students to the field of neuroimaging genomics, characterizing large-scale genomic and imaging datasets to uncover relationships between imaging features, molecular genomic profiles, and phenotype.
| Units: 3
BIOS 232:
Two-photon Imaging of Neural Circuits
Focuses on application of two-photon imaging to modern neuroscience. Topics include microscopy and imaging.
Last offered: Winter 2016
| Units: 2
BIOS 233:
Experimental Metagenomics: Nectar Microbes as a Model System
Preference to graduate students and post-docs; open to upper-level undergraduates with instructor consent. Emphasis on developing a practical understanding of how to conduct metagenomic research by combining cutting-edge molecular sequencing with experimental ecological approaches. Focuses on the community ecology of the bacterial and yeast species that colonize floral nectar via pollinators and the implications for plant-pollinator interactions within an agriculturally relevant framework. Ecological, evolutionary, and phylogenetic principles and microbiological and molecular techniques that will be taught are broadly applicable in many biological fields, including the medical ecology of hte human microbiome. Inquiry-based with individual student-led projects.
| Units: 3
BIOS 234:
Personalized Genomic Medicine
Focuses on next-generation sequencing and its implications for personalized genomic medicine. Students gain hands-on experience with popular DNA sequence analysis tools as well as a practical understanding of the underlying algorithms and biomedicine.
Last offered: Spring 2016
| Units: 1
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
| Units: 2
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
| Units: 4
BIOS 237:
Investigating Biology with Fluorescent Proteins
Focuses on fluorescent proteins, a proven research tool for imaging a wide range of biological phenomena and continuously uncover exciting discoveries in many areas. Students gain practical expertise in concepts, methodology, and data analysis through lectures, literature discussion, and hands-on computer exercises with "real world" data.
Last offered: Winter 2015
| Units: 1
BIOS 238:
Quantitative single cell analysis of live cell images
Last offered: Autumn 2014
| Units: 1
BIOS 239:
Synapse Development
Focuses on the mechanisms of synapse development, including the role of adhesion molecules in establishing neuronal contacts, the function of synapse-inducing molecules, how pre- and postsynaptic material is transported to nascent synapses, synapse maturation, synapse elimination as well as how synaptic dysfunction may lead to neurological disorders. Readings from primary literature.
Last offered: Winter 2015
| Units: 3
BIOS 240:
Cellular Metabolism: An Emerging Hallmark of Cancer and Aging
Introduction to cellular metabolism, including changes in metabolic flux that drive diverse disease states from cancer to aging. Topics covered include cancer metabolism, cellular nutrient sensing, metabolism in aging, and the influence of metabolism on stem cell fate. This course uses discussion of recent advances in the field to place an emphasis on practical applications, including the integration of metabolomics into the era of ¿Big Data¿. This mini-course culminates with a lab section allowing the students to conduct an extracellular flux experiment using the Seahorse analyzer to study changes in mitochondrial respiration and glycolysis in cancer cells.
Last offered: Winter 2015
| Units: 1
BIOS 241:
Dissecting algorithms for RNA Sequencing
Class focuses on a few popular and commonly used algorithms for RNA-Seq analysis. The course dissects the algorithmic assumptions, statistical methods they use to test hypotheses about RNA expression and evaluates properties such as robustness, sensitivity and specificity, highlighting some large "blind spots" in many algorithms.
Last offered: Winter 2015
| Units: 2
BIOS 242:
Writing Compelling Fellowships and Career Development Awards
An overview of principles and fundamentals for writing competitive fellowships (e.g. NIH F31, F32) and career development awards (e.g. NIH K Awards). Topics include: developing specific aims and career development plans; using the review criteria to inform writing; timelines and resources. Participants develop proposals through guided exercises with an emphasis on in-class peer review and focused faculty feedback.
Terms: Aut
| Units: 2
BIOS 243:
Grant Writing Academy Mini Course: Specific Aims
Concise overview of the fundamentals for writing competitive NIH Kirschtein NRSA fellowships (F31, F32) and K Awards. Topics include developing specific aims; outlining research and career development plans; and using the review criteria to inform writing. Participants develop their one-page NIH-Specific Aims document with an emphasis on in-class peer review and protected daily proposal writing. Students enroll for units in one small-group section, and also attend two mandatory lectures as noted in class schedule.
Last offered: Summer 2016
| Units: 1
BIOS 244:
Computer Applications in Pharmaceutical Research and Development
After a brief introduction to drug discovery and development process in pharmaceutical industry, we discuss integrative computational approaches to drug discovery, development, and marketing. Illustrative case studies and examples explain how applications are used at various stages, including bioinformatics, data mining, high-throughput screening, predicting human response to drugs, and adverse drug event monitoring.
Last offered: Spring 2016
| Units: 1
BIOS 245:
The Immune Response to Infectious Diseases
Focuses on the immune defenses that the human body uses to prevent and control infectious diseases. Covers both innate and adaptive immune defenses against bacterial, fungal, and viral pathogens will be covered. This course is targeted primarily at graduate students and postdocs whose primary focus is not in immunology, but whose research and interests intersect with the host response to infectious diseases. Motivated undergraduates may also participate.
Last offered: Winter 2016
| Units: 1
BIOS 246:
Introduction to Meta-Analysis
Meta-analysis is the quantitative synthesis and analysis of a collection of independent studies. It provides a more objective and powerful way of summarizing evidence across studies than descriptive reviews. The importance and utility of this quantitative method for answering new questions and synthesizing existing results in different fields of scientific research is demonstrated by the dramatic increase in the number of studies using meta-analysis in the last ten years. Focuses on the basics of meta-analysis. The emphasis of the course is both on the conceptual understanding and practical use of this method, as applied to biological questions.
Last offered: Spring 2016
| Units: 4
BIOS 247:
Neuro-Cellular Core
Focus on fundamental aspects of cellular neurophysiology. Topics include: electrophysiological properties of neurons; synaptic structure and function; synaptic plasticity; didactic lecture component and student-led discussion of classical papers. Students use the simulation program Neuron.
| Units: 2
BIOS 248:
Scientific Computing for Ecologists, Biologists and Environmental Scientists
One-week intensive course is specifically dedicated to graduate students and postdocs in Biology and Environmental Science eager to be introduced to, and get proficient in, scientific computing. Focus is on acquiring the necessary skills to boost their productivity by learning state-of-the-art and cutting-edge techniques to retrieve and process big data. Course introduces Unix/Linux, R, ggplot2 graphic package, regular expressions and version control, dynamic reporting generation through hands-on and interactive learning opportunities both during lectures and in extensive lab sessions based on real world case studies extracted from published papers.
Last offered: Autumn 2015
| Units: 3
BIOS 249:
Interactive Microbiology
Focus is on phototactic behavior of single celled organisms and the biophysical principles of feedback control and hydrodynamics underlying it. Enables real biology experimentation in the cloud, and is ultimately intended to illustrate and teach the scientific method (free exploration, hypothesis formation, measurement, data analysis, modeling, conclusions).
Last offered: Winter 2016
| Units: 1
BIOS 250:
Interdisciplinary Drug Discovery
Focuses on decision making in science, with particular attention to skills for identifying when to solicit interdisciplinary input, and how to guide such discussions to productive endpoints. Uses case studies based on Novartis projects to teach ways to leverage interdisciplinary knowledge, effectively communicate across disciplines, and drive teams to decision points. Two-day workshop presented by Novartis scientists who lead participants through these real life examples of interactive teams within pharma solving problems through collaborative decision making. Participants develop collaborative decision making skills highlighted through group exercises.
Terms: Aut
| Units: 1
BIOS 251:
Biotechnology in the Natural World (SBIO 251)
Life can be found in some of the strangest and most inhospitable places of Earth. Whether in hot springs, oceanic depths, or dense rainforests, living organisms must be natural specialists to survive. This course explores a selection of strange and ingenious biomolecules that natural organisms have evolved in order to survive. Lectures will cover historical background as well as detailed investigations of the structure and function of selected biomolecules of interest. The majority of each lecture and discussion will focus on the adaptation of those molecules for fundamental and innovative approaches in modern biotechnology, especially in medicine and biophotonics. Key biophysical and biochemical techniques will be discussed as they are encountered within primary literature.
Terms: Win
| Units: 1
BIOS 252:
Experimental strategies for understanding plant-environmental responses
This minicourse will explore the specific aspects of the environment that plants sense, the impacts these stimuli have on plant physiology and the state-of-the-art in experimental methods used to study plant-environmental interactions. Each week will include a lecture, group discussion and lab focused on one of three key environments: the soil, canopy and agricultural field. Lectures will provide necessary background information, literature-based discussions will evaluate current methods and identify areas where innovation is needed, and labs will include demonstrations of several common methods and a trip to the Salinas Valley to visit a farm.
Terms: Win
| Units: 1
BIOS 253:
Discovery and Innovation in Emerging Viral Infections
An interdisciplinary mini course focused on challenges posed by emerging viruses and innovative efforts to overcome them. Modules include epidemiology and ecology of emerging viral infections, such as Ebola, dengue, and Zika, discovery of new emerging viruses, development and application of molecular assays for the diagnosis and management of emerging viral infections, bioinformatics and genetic approaches for antiviral target discovery, and novel therapeutic approaches for combating emerging viruses. It is intended for graduate students and postdoctoral fellows interested in emerging viral infections. Advanced undergraduates are also welcome. Prerequisite: background in molecular biology.
Terms: Win, Spr
| Units: 1
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: Spr
| Units: 2
BIOS 255:
Promises and Pitfalls: A Critical Evaluation of Neuroscience Techniques
The complexity of modern neuroscience requires researchers to develop an interdisciplinary approach. This course explores multiple technologies for understanding the brain and is less a survey of different techniques than a critical comparison of them. With the goal of incorporating a new technique into their own research projects, students will address potential advantages, disadvantages and limitations of various methods. The final two class meetings will be devoted to allowing students to develop a plan to integrate a new technique into their current research projects and receive feedback from the class on how informative and viable their plans may be.
Terms: Win
| Units: 1
BIOS 256:
SCULPTURAL DATA ILLUSTRATIONS
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
| Units: 1
BIOS 257:
HIV: The virus, the disease, the research
Medical students, graduate students in biological sciences, undergraduate students with strong biological background. Topics: Immunopathogenesis, immune deficits, opportunistic infections including TB, and malignancies; Genomics viral genetic analyses that have traced the origin of HIV-1 and HIV-2 to primates, dated the spread of infection in humans, and characterized theevolution of virus within infected individuals; Antiretroviral drug development identification of drug targets, structure-based drug design, overcoming drug resistance; Challenges of vaccine development; Public health strategies
Terms: Spr
| Units: 1
BIOS 258:
Ethics, Science, and Society
This discussion focused Ethics, Science, and Society interactive mini course will engage Biosciences graduate students 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.
Terms: Win, Sum
| Units: 1
BIOS 259:
Statistical Genetics of Complex Traits
This course provides an overview of statistical methods for analyzing human genetic variation and for understanding the genetic basis of complex traits. Topics include: principles of population genetics; effects of evolutionary forces on pattern of genomic variation; epidemiologic designs; genotype-phenotype association analyses of complex traits; missing heritability. Weekly interactive computing sessions will provide guided exercises analyzing real genomic data. Pre-requisite: basic understanding of probability and access to a laptop computer.
Terms: Win
| Units: 1
BIOS 260:
Principles of Quantitative Biological Microscopy and Image Analysis
Lectures and laboratories emphasizing hands-on experience. Microscopy topics include microscope optics, resolution limits, Koehler illumination, fluorescence microscopy, confocal, TIRF, FRET, photobleaching and super-resolution. Image analysis topics include using CellProfiler, ImageJ, and MATLAB scripts to carry out segmentation and analyze subcellular localization, RNA FISH, live cell-cycle dynamics, and cell tracking. Prerequisite: basic physics.
| Units: 2
BIOS 261:
Plant anatomy and cellular structure: fundamental concepts to interpret data
Plant anatomy and cell biology. This two-week mini course will introduce the cell types of major organ systems in flowering plants through lectures and readings. Classic and modern techniques to highlight plant cell structures and dynamic processes such as changes in hormone concentration and microtubule dynamics will be presented in laboratory sections immediately following each lecture. Limited to 8 registered students. Graduate students only. Course is not open to undergraduates.
Terms: Sum
| Units: 2
BIOS 262:
Learning to Fly: Drosophila Research Methods
This week-long course will be an overview of the fly as a model system, and the tools available to fly researchers. It will cover topics like history, anatomy, development, online databases, genetic toolkits, genome editing techniques, and stem cell, immunology, and neural research methods. Lectures will be given by experts in the field, who will also be encouraged to discuss the advantages and disadvantages of the fly, as well as how this model system differs from vertebrate systems. We will also provide an optional 2-hour lab that will expose students who have little fly experience to basic fly techniques.
Terms: Spr
| Units: 1
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
| Units: 2
| Repeatable
10 times
(up to 20 units total)
BIOS 264:
Introduction to Data Management and Analysis for Genomics Research
This practical, interactive workshop will introduce participants to concepts, skills and tools for effective management and analysis of genomics data using R, an open source programming language. Topics will include cloud computing for genomics, the command line, data wrangling and processing, and data analysis and processing in R. Students will engage in hands on analyses of genomics data using the Data Carpentry workshop format (see datacarpentry.org). Participants must bring their own laptop, and should plan to participate actively. This class is for any researcher who has data they want to analyze. No prior computational experience is required.
Terms: Win
| Units: 1-2
