Print Settings
 

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 204: Modeling Cell Signaling

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: Aut | Units: 3
Instructors: ; Ferrell, J. (PI)

BIOS 215: Stanford SKY Campus Happiness Retreat

Discover the power of the breath to reach a meditative state of mind. Combine meditation with activities that inspire connection and purpose through community building and mindful leadership. Learn through breathwork, meditation, lecture, class discussion, experiential learning, and yoga. The cornerstone of the course is evidence-based SKY Meditation technique that uses the breath to quiet the mind, supporting a deep experience of meditation and a practical approach to happiness.
Terms: Aut | Units: 1 | Repeatable 3 times (up to 3 units total)

BIOS 217: Foundations of statistics and reproducible research

Introduction to foundations of rigorous, reproducible research in experimental biology and clinical research. Provides conceptual framework for linking hypotheses to experimental design, quantitative measurement, statistical analysis and assessment of uncertainty. Course combines lecture presentation and discussion of core concepts from statistics and reproducibility with hands-on exposure to best practices for reproducible workflows spanning design, data collection, annotation, analysis and presentation of results. Brief discussion of social, legal, and ethical issues with reproducibility in scientific practice, along with NIH grant requirements. Course provides foundations for future learning in these areas. Examples drawn from multiple areas of experimental biology and clinical research. Target audience: Students in BIOS 200 (Foundations in Experimental Biology), in Biosciences graduate programs or T32 training programs. Prerequisites: None
Terms: Aut | Units: 2
Instructors: ; Goodman, S. (PI)

BIOS 219: Early Development Strategies for Neutralizing Antibodies and Brain Permeable Small Molecules

This course will provide students with an overview of current technologies related to the development of small molecules and neutralizing antibodies. Delivered via classroom instruction and a workshop, these modules will aim to increase the fundamental understanding of drug development terminology and processes, combined with real-world examples of discovery therapeutics and technologies developed for translation to clinic. Emphasis will be made on the development of small molecules that can cross the blood-brain barrier and show potential for translation in clinic. Focus will also be put on the screening of antibody targets followed by target validation, target profile development and preclinical evaluation. The workshop will focus on computational molecular docking which is an excellent tool that will help reduce the attrition rate during the drug development process and lead identification studies. Active engagement of the students during the workshop is expected based on the need to install specific software and completion of assigned tasks (computational docking). Students are expected to bring personal laptops to class on day 1 and 2 to perform docking exercises.
Terms: Aut, Win | Units: 1

BIOS 221: Modern Statistics for Modern Biology (STATS 256, 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: Working knowledge of R and two core Biology courses. Note that the 155 offering is a writing intensive course for undergraduates only and requires instructor consent. (WIM). See https://web.stanford.edu/class/bios221/index.html
Terms: Aut | Units: 3

BIOS 223: Development and reporting of robust and reproducible LC-MS/MS assays

This mini-course offers a series of lectures and hands-on labs to discuss the development and reporting of reproducible quantitative LC-MS/MS molecular assays using a triple quadrupole. We will discuss chromatography and mobile phase selection, mass spectrometry parameters and selection of fragment ions, and the reporting and interpretation of published methods. Additionally we will cover the use of internal standards and sample preparation, and normalization methods for reproducible data analysis. Students will have the opportunity to work with a mass spectrometer and will design a cohesive plan for a targeted assay of an example molecule in their research.
Terms: Aut, Win | Units: 1

BIOS 229: Open Source Prototyping: Translating Ideas to Reality using Rapid Prototyping Methods

"Open Source Prototyping" is a hands-on course that equips students with the skills and knowledge to use open-source design tools and rapid prototyping technologies, such as 3D printing and CNC. Students will learn how to translate their ideas into real-world objects, understanding the full process from ideation to realization. Key topics include navigation of leading design software, 3D printing technologies, and in-depth understanding of materials science. The course emphasizes open-source principles, and their applications in additive manufacturing. It features a wide range of applications, including medical devices, lab equipment, and experimental apparatuses, providing a comprehensive look at prototyping potential.
Terms: Aut, Spr | Units: 1
Instructors: ; Wang, B. (PI)

BIOS 230: Successful Fieldwork in Global Health Research

This two-day workshop focuses on how to successfully implement fieldwork in global health research. After this class, students will have a detailed plan for their fieldwork, including entering and exiting the field, ethical concerns, impact, safety, equitable partnerships, and preparing for the unexpected. The course builds on student-led active learning techniques, with invited guest speakers who share their fieldwork experiences. The course is open to advanced graduate students and postdocs who have developed a research question and design for global health research. Students are recommended but not required to take the course ¿Practical Approaches to Global Health Research¿ (MED226/INTLPOL290/EPI237) beforehand.
Terms: Aut | Units: 1

BIOS 235: Foundations of Computer Science: What the Tutorial Didn't Tell You

The course provides non-computer-science students with a comprehensive understanding of computer science and software engineering principles for efficient code in modern scientific computing. Students gain theoretical knowledge and practical skills to advance programming proficiency and develop robust software systems. Upon completion, students have foundational knowledge in computer science, capable of writing better code for scientific computing. They gain expertise in selecting tools, designing modular software systems, and following best coding practices. They understand the importance of testing and version control in software development, ready to tackle advanced programming challenges in scientific applications. Prerequisites: Familiarity with a high-level programming language. More info and sign up at: https://forms.gle/qJSL1PBdokaUTLV6A
Terms: Aut | Units: 2

BIOS 237: Engineering Wellness

This 3-week course will help students understand how lifestyle and wellness choices impact physiology using a data-driven approach powered by wearable technology. Each student will be given an Oura ring to use during the course. On Mondays and Wednesdays, we will learn evidence-based practices for mental health and well-being, and on Fridays engineers from Oura, Apple, and Fitbit will teach the students about wearable data sensors and analysis. Students will assess their own smartwatch data to look at real-time physiological responses to wellness interventions such as exercise, awareness meditation, laughter yoga, and inquiry-based stress reduction. This course will bring in academic experts and popular wellness leaders. Last year's teachers included Byron Katie, Deepak Chopra, MD, Madan Kataria, MD the founder of Laughter Yoga, Michael Snyder, PhD, James Doty, PhD, Lindsay Briner, and George Slavich, PhD, to learn about cutting edge research and innovation in mental health, and to experience these practices firsthand through immersive workshops. The capstone project of the course will involve analyzing your own personal wearable device data to quantify the physiological impact of BIOS 237. Due to the high demand for this unique three-week course, we are accepting students on a first-come, first-served basis. Complete and confirm the form promptly to secure your spot: https://forms.gle/TRMRJJ1qHA8MypF79 Learn more at engineeringwellness.stanford.edu.
Terms: Aut, Win | Units: 2 | Repeatable 2 times (up to 4 units total)

BIOS 241: Data Wrangling with Bash

This one week course workshops writing bash scripts to reproducibly clean-up and transform raw data for analysis. Topics include introduction to bash, command-line tools for data manipulation, and best practices for scripting. Students will automate conversion of their own raw data to an input format for analysis. No prerequisites.
Terms: Aut | Units: 1

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 249: Single-cell Spatial-omics: with Applications to Stem Cell Engineering and Cancer Immunotherapy

With many technological breakthroughs in the past decade, single-cell biology has blossomed in many fields, enabling us to ask questions that were not possible before. However, many of the single-cell biology technologies include a dissociation step, which destroys the crucial spatial information. Therefore, a new wave of technology focusing on single-cell spatial-omics emerges to overcome this challenge. This course will explore seminal and new experimental and computational strategies employed in both the conventional single-cell omics and the new single-cell spatial-omics, emphasizing applications to stem cell engineering and cancer biology. We will teach you how to design and analyze single cell-omics data, using questions and data from stem cell biology and cancer biology to provide the motivational background. Basic stem cell and cancer biology will be covered. Pivotal studies regarding cell identity and single-cell biology will drive discussion on the fidelity of engineered cell populations and the challenges of understanding cell fate decisions.
Terms: Aut | Units: 2

BIOS 250: An Introduction to Mathematical Modeling for Ecology

This course provides an introduction to understanding, creating and analyzing mathematical models in ecology. We will cover different types of mathematical models, as well as their components, with a focus on foundational models in ecology, such as the Leslie population model, the Lotka-Volterra predator-prey model and SIR disease models. By the end of the course, you will be able to formulate and modify equations, and create diagrams to describe well-defined ecological processes. Finally, you will be able to use simple algebra and R to explore model results. No prior experience is required.
Terms: Aut | Units: 1
Instructors: ; Pourtois, J. (PI)

BIOS 253: Primary concepts in Bioinformatics- To Make Sense Of large scale Biological and Biomedical Data

Every biological problem to be nowadays in cancer biology, stem cell research, biological drug discovery or predictive disease modeling requires a large-scale bioinformatics analysis to make deeper insights leading to therapeutics and drug development. This course will start with a brief introduction in bioinformatics and then focus on key computational techniques and algorithms used to studying different areas like Genome Wide Association studies in psychiatric disorders, supervised and unsupervised machine learning approaches to make sense of biological image, single-cell perturbation data to biomarker discovery in cancer. The course will have some hands-on analysis components with both bulk and single cell RNA sequencing data with context to some disease models and organismal systems.
Terms: Aut | Units: 1-3 | Repeatable 2 times (up to 6 units total)
Instructors: ; Goswami, A. (PI); Mam, B. (SI)

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 | Units: 2
Instructors: ; Goodman, M. (PI)

BIOS 255: Solar energy conversion and storage

This course introduces different technologies for harvesting and storing solar energy, the most abundant source of renewable energy on earth. This course will cover ways to generate electricity (solar cells) and molecular fuels (biofuels and solar fuels) and the key solutions for short and long-term solar energy storage, including batteries, supercapacitors, electrolyzers, and fuel cells. For each topic, we will cover the existing and emerging technologies, how they work, what role they fill in the energy transition, and how they need to be improved. Students will give a final presentation where they cover a technology or proposed technology of their choosing.
Terms: Aut | Units: 1

BIOS 258: Reproducibility through effective coding and data management

This course introduces science reproducibility through effective coding and data management. Students will complete team projects on a statistical or simulation topic of their choosing and publish them on GitHub. Instructors will guide students in learning to use R, R markdown, and GitHub to collaborate with peers as they advance their project. By the end of the course, students will learn effective coding practices, data management, version control and collaboration, and sharing analytical results. The course aims to provide students with the tools and knowledge to help make their research reproducible and easily accessible. No prerequisites required.
Terms: Aut | Units: 3
Instructors: ; Nell, L. (PI); Warren, M. (PI)

BIOS 260: Peds Endo Journal Club Course

The Pediatrics Endocrinology Journal Club Course aims to provide a platform for trainees in the division to discuss key literature discoveries in the general field of endocrinology and diabetes. Each student will discuss with the primary instructors to determine a topic or a specific research article to present. In each class, one student will present an introduction of their topic of choice in the first half. In the second half, the primary instructors will serve as facilitators to engage the group and discuss details and future directions of the topic.
Terms: Aut | Units: 1-3

BIOS 261: Rigor and reproducibility in biological research: collection, analysis and use of biological data

The deluge of data common in modern biological research poses new challenges for ensuring reproducibility and collaboration at many levels. High-powered computational and statistical tools are becoming as indispensable as pipettes and flasks, demanding a rethinking of what it means to be rigorous and reproducible in the generation, visualization, and interpretation of results. In this mini-course, we will explore key concepts in how data should be stored, analyzed, manipulated, and presented using computational tools such as the Python programming language and GitHub version control software at a hands-on level, guiding students through a mini research project. This is an introductory course that assumes no previous knowledge of programming or statistics, and is especially relevant for students or postdocs interested in developing a skill set for quantitative biology.
Terms: Aut | Units: 2

BIOS 264: Answering biological questions with Metagenomic Data

Metagenomic datasets capture the full genomic complement of microbial communities within a sample and thus have broad applications in environmental microbiology, human health, and evolutionary biology. In this three-week minicourse, students will learn both the principles and practice of metagenomics, implementing a standard computational workflow that begins with sequencing reads and concludes with basic genome analysis. Students will also gain hands-on experience with the command line, high-performance computing, and common bioinformatic tools/data types. Overall, the course will teach students how to interrogate metagenomic data to answer questions about microbial diversity, abundance, and gene content. It is open to those with any level of programming experience.
Terms: Aut | Units: 1
Instructors: ; Jaffe, A. (PI)

BIOS 272: Science and Art

This 3-week mini-course will cover a variety of topics related to science and art including scientific illustration, the visual sensory perception of art, how art impacts the brain, and the similarities and differences between science and art. The class will be a combination of lectures, discussions, and art labs. No previous art experience is necessary.
Terms: Aut, Win | Units: 1

BIOS 273: Ethics and Justice at the Frontiers of Conservation Biology

This weekend-long retreat-style mini-course introduces students to four distinct types of cross-disciplinary ethical challenges that will face the next generation of conservation biologists and biotech entrepreneurs. Taught over the course of a single long weekend, students will wrestle with vexing questions of scientific ethics, interspecies justice, environmental justice, and policy. We will employ structured debates, stakeholder role-play, site visits to conservation-tech companies, and outings to local conservation areas. This course will be co-taught by guest instructor Ben Wilcox from World Wildlife Fund. We can accept up to 20 students; to be considered, please fill out this form to explain your interest in the course: http://tinyurl.com/BIOS273
Terms: Aut | Units: 2

BIOS 277: Prions in Health & Disease

Prions consist of misfolded, polymerized proteins and are agents of transmissible neurodegenerative diseases such as bovine spongiform encephalopathy and Creutzfeldt-Jakob disease of man. However, "prion-like" polymerization of proteins is a more general phenomenon involved in a long-term memory, innate immunity and most likely other important functions. In microbes, prions are non0Mendelian genetic elements. The course will emphasize that "prion-like" polymerization is part of a more general allosteric regulation of gene expression that can sometimes go wrong, as in Alzheimer's and Parkinson's diseases, and only exceptionally may cause transmissible infectious disease that spread in the population.
Terms: Aut | Units: 1

BIOS 287: Proteostatis: guarding the proteome in health and disease

The control of cellular protein homeostasis, also called Proteostasis, is emerging as the central cellular process controlling the stability, function and quality control of the proteome and central to our understanding of a vast range of diseases. The proteostasis machinery maintains the function of destabilized and mutant proteins; assists the degradation of damaged and aggregated proteins and monitors the health of the proteome, adjusting it in response to environmental or metabolic stresses. This class will introduce students to the exciting cutting edge discoveries in this field, and will relate them to medical and biotechnology applications, as well as how a better understanding of proteostasis can be leveraged to understand fundamental biological processes, such as evolution and aging and to ameliorate a wide range of diseases. Given the increasingly close links between aging, protein misfolding, and neurodegenerative disease, understanding proteostasis networksis of critical fundamental and practical importance. These insights are particularly relevant in view of the increased prevalence of late-onset neurodegenerative aggregation diseases caused by an increasingly elderly population.
Terms: Aut | Units: 3

BIOS 290: Preparation & Practice: Law

Through tailored lecture, case study and a practical final project, Biosciences and interdisciplinary sciences students and trainees will learn how to apply the skills they acquired in their academic training to a career in Patent Prosecution and related fields. Taught by field and faculty experts, this is your opportunity to network with IP law representatives and to gain hands-on experience in a new career of choice option. Topics include: applying for positions, the importance of IP protection, licensing, overview of the patent process, drafting applications and litigation.
Terms: Aut | Units: 1

BIOS 294: Chemistry for Biologists and Others (BIOC 294)

Chemical transformations are central to biology and function, and chemical methods provide some of the most powerful tools for everyday experimental biology. Yet, most practitioners of biology have learned chemistry through memorization and do not use chemical principles or intuition in their research, even though chemistry underlies most processes and experiments carried out in biology and by biologists. Fortunately, a basic understanding and working knowledge can be gained in a short time, through a small set of simple concepts and limited number of memorized facts. These concepts and facts will be introduced and then mastered through use in highly interactive, in-class problems and evaluation of selected literature. At the end of the three-week course students will have an ability to understand the chemistry underlying cellular processes and to better discuss and evaluate chemical tools and approaches. Prerequisites: High school or college introductory chemistry recommended but not required.nnCourse runs 11/15-12/10 MWF 10-11:45am
Terms: Aut | Units: 3

BIOS 295: Statistical Methods and Data analysis for Clinical Research

This mini-course will introduce students to the basic concepts and methods of biostatistics and how they are applied to analysis and interpretation of data in clinical research. Topics will include: Study designs: Observational studies and Clinical trials, Bias and confounding during study design and analysis phases, Hypothesis formulation and Power analysis, Data collection and management, Descriptive and Inferential statistics, Hypothesis testing: Data analysis, interpretation, and presentation, Role of Research Rigor and reproducibility. Students will learn how to use statistical software to analyze data and draw conclusions from their analyses. They will also learn how to communicate their findings to others in a clear and concise way.
Terms: Aut, Win | Units: 1
Instructors: ; Kamtam, D. (PI)

BIOS 298: Cinematic Discoveries: A movie-based exploration of research rigor, communication and diversity

Through movie depictions of the vaccine discoveries leading to the first Nobel prizes in medicine, the infamous Tuskegee Study, the first heart surgery for Tetralogy of Fallot, the encephalitis lethargica pandemic, and modern oncology trials, the course will explore interdisciplinary work in biomedical sciences, research rigor, consent, stigma and discrimination, researchers¿ and health professionals¿ communication skills, and fundamentals of cinematography. The course will include a lecture, a movie projection and discussion each day for 5 days.
Terms: Aut | Units: 1

BIOS 299: Online Proposal Bootcamp

This 9-week Proposal Bootcamp guides grant writers through the process of developing a compelling fellowship (e.g., NIH F31, F32) or career development award (e.g., NIH K99/R00, K01, K08, etc.). Participants gain new grant writing skills through synchronous, including Mini Lectures and Grant Coach Office Hours, and asynchronous, including recorded videos and readings, activities. Students and postdocs join our award-winning peer review program for feedback on key proposal documents. This Bootcamp is 100% remote and open to all Stanford affiliates.
Terms: Aut, Spr | Units: 2 | Repeatable 2 times (up to 4 units total)
Instructors: ; Botham, C. (PI)

BIOS 301: Graduate Environment of Support

Psychosocial, financial, and career issues in adapting graduate students to Stanford; how these issues relate to diversity, resources, policies, and procedures. Discussions among faculty, advanced graduate students, campus resource people, and the dean's office. (Thomas)
Terms: Aut | Units: 1
Instructors: ; Thomas, A. (PI)
© Stanford University | Terms of Use | Copyright Complaints