Results for BIOE

This seminar is for anyone who loves food, cooking or science! We will focus on the science and biology behind the techniques and the taste buds. Not a single lecture will pass by without a delicious opportunity - each weekly meeting will include not only lecture, but also a lab demonstration and a chance to prepare classic dishes that illustrate that day's scientific concepts.

BIOE 42 is designed to introduce students to general engineering principles that have emerged from theory and experiments in biology. Topics covered will cover the scales from molecules to cells to organisms, including fundamental principles of entropy, diffusion, and continuum mechanics. These topics will link to several biological questions, including DNA organization, ligand binding, cytoskeletal mechanics, and the electromagnetic origin of nerve impulses. In all cases, students will learn to develop toy models that can explain quantitative measurements of the function of biological systems. Prerequisites: MATH 19, 20, 21 CHEM 31A, B (or 31X), PHYSICS 41; strongly recommended: CS 106A, CME 100 or MATH 51, and CME 106; or instructor approval.

Introduction to next-generation techniques in genetic, molecular, biochemical, and cellular engineering. Lab modules build upon current research including: gene and genome engineering via decoupled design and construction of genetic material; component engineering focusing on molecular design and quantitative analysis of experiments; device and system engineering using abstracted genetically encoded objects; and product development based on useful applications of biological technologies. Concurrent or previous enrollment in BIO 82 or BIO 83.

Fundamental human anatomy, spanning major body systems and tissues including nerve, muscle, bone, cardiovascular, respiratory, gastrointestinal, and renal systems. Explore intricacies of structure and function, and how various body parts come together to form a coherent and adaptable living being. Correlate clinical conditions and therapeutic interventions. Participate in lab sessions with predissected cadaveric material and hands-on learning to gain understanding of the bioengineering human application domain. Encourage anatomical thinking, defining challenges and opportunities for bioengineers.

BIOE 70Q invites students to apply design thinking to the creation of healthcare technologies. Students will learn about the variety of factors that shape healthcare innovation, and through hands-on design projects, invent their own solutions to clinical needs. Guest instructors will include engineers, doctors, entrepreneurs, and others who have helped bring ideas from concept to clinical use.

Students completing BIOE.80 should have a working understanding for how to approach the systematic engineering of living systems to benefit all people and the planet. Our main goals are (1) to help students learn ways of thinking about engineering living matter and (2) to empower students to explore the broader ramifications of engineering life. Specific concepts and skills covered include but are not limited to: capacities of natural life on Earth; scope of the existing human-directed bioeconomy; deconstructing complicated problems; reaction & diffusion systems; microbial human anatomy; conceptualizing the engineering of biology; how atoms can be organized to make molecules; how to print DNA from scratch; programming genetic sensors, logic, & actuators; biology beyond molecules (photons, electrons, etc.); what constraints limit what life can do?; what will be the major health challenges in 2030?; how does what we want shape bioengineering?; who should choose and realize various competing bioengineering futures?

Physiology of intact human tissues, organs, and organ systems in health and disease, and bioengineering tools used (or needed) to probe and model these physiological systems. Topics: Clinical physiology, network physiology and system design/plasticity, diseases and interventions (major syndromes, simulation, and treatment, instrumentation for intervention, stimulation, diagnosis, and prevention), and new technologies including tissue engineering and optogenetics.  Discussions of pathology of these systems in a clinical-case based format, with a view towards identifying unmet clinical needs.  Learning computational skills that not only enable simulation of these systems but also apply more broadly to biomedical data analysis. Prerequisites: CME 102; PHYSICS 41; BIO 82, BIO 84.

*ONLINE Offering of BIOE 103. This pilot class, BIOE103B, is an entirely online offering with the same content, learning goals, and prerequisites as BIOE 103. Students attend class by watching videos and completing assignments remotely. Students may attend recitation and office hours in person, but cannot attend the BIOE103 in-person lecture due to room capacity restraints.* Physiology of intact human tissues, organs, and organ systems in health and disease, and bioengineering tools used (or needed) to probe and model these physiological systems. Topics: Clinical physiology, network physiology and system design/plasticity, diseases and interventions (major syndromes, simulation, and treatment, instrumentation for intervention, stimulation, diagnosis, and prevention), and new technologies including tissue engineering and optogenetics. Discussions of pathology of these systems in a clinical-case based format, with a view towards identifying unmet clinical needs. Learning computational skills that not only enable simulation of these systems but also apply more broadly to biomedical data analysis. Prerequisites: CME 102; PHYSICS 41; BIO 82, BIO 84. strongly recommended PHYSICS 43. Enrollment with Instructor approval

Bioengineering focuses on the development and application of new technologies in the biology and medicine. These technologies often have powerful effects on living systems at the microscopic and macroscopic level. They can provide great benefit to society, but they also can be used in dangerous or damaging ways. These effects may be positive or negative, and so it is critical that bioengineers understand the basic principles of ethics when thinking about how the technologies they develop can and should be applied. On a personal level, every bioengineer should understand the basic principles of ethical behavior in the professional setting. This course will involve substantial writing, and will use case-study methodology to introduce both societal and personal ethical principles, with a focus on practical applications.

Directed study and research for undergraduates on a subject of mutual interest to student and instructor. Prerequisites: consent of instructor and adviser. (Staff)

Individual research by arrangement with out-of-department instructors. Credit for 191X is restricted to declared Bioengineering majors pursuing honors and requires department approval. See http://bioengineering.stanford.edu/education/undergraduate.html for additional information. May be repeated for credit.

For undergraduate students participating in the Stanford ChEM-H Undergraduate Scholars Program. This course will expose students to interdisciplinary research questions and approaches that span chemistry, engineering, biology, and medicine. Focus is on the development and practice of scientific reading, writing, and presentation skills intended to complement hands-on laboratory research. Students will read scientific articles, write research proposals, make posters, and give presentations.

This course exposes students to the engineering principles and clinical application of medical devices through lectures and hands-on labs, performed in teams of two. Teams take measurements with these devices and fit their data to theory presented in the lecture. Devices covered include X-ray, CT, MRI, EEG, ECG, Ultrasound and BMI (Brain-machine interface). Prerequisites: BIOE 103 or BIOE 300B.

Capstone Biomedical Data Science experience. Hands-on software building. Student teams conceive, design, specify, implement, evaluate, and report on a software project in the domain of biomedicine. Creating written proposals, peer review, providing status reports, and preparing final reports. Issues related to research reproducibility. Guest lectures from professional biomedical informatics systems builders on issues related to the process of project management. Software engineering basics. Because the team projects start in the first week of class, attendance that week is strongly recommended. Prerequisites: BIOMEDIN 210 or 214 or 215 or 217 or 260. Preference to BMI graduate students. Consent of instructor required.

Theoretical analysis of dynamical processes: dynamical systems, stochastic processes, and spatiotemporal dynamics. Motivations and applications from biology and physics. Emphasis is on methods including qualitative approaches, asymptotics, and multiple scale analysis. Prerequisites: ordinary and partial differential equations, complex analysis, and probability or statistical physics.

Preference to graduate students. Focus is on the human gut microbiota. Students enrolling for 3 units receive instruction on computational approaches to analyze microbiome data and must complete a related project.

The physical and chemical basis of macromolecular function. Topics include: forces that stabilize macromolecular structure and their complexes; thermodynamics and statistical mechanics of macromolecular folding, binding, and allostery; diffusional processes; kinetics of enzymatic processes; the relationship of these principles to practical application in experimental design and interpretation. The class emphasizes interactive learning, and is divided equally among lectures, in-class group problem solving, and discussion of current and classical literature. Enrollment limited to 30. Prerequisites: Background in biochemistry and physical chemistry recommended but material available for those with deficiency in these areas; undergraduates with consent of instructor only.

Concepts and techniques for the design and implementation of engineered genetic systems. Topics covered include the quantitative exploration of tools that support (a) molecular component engineering, (b) abstraction and composition of functional genetic devices, (c) use of control and dynamical systems theory in device and systems design, (d) treatment of molecular "noise", (e) integration of DNA-encoded programs within cellular chassis, (f) designing for evolution, and (g) the use of standards in measurement, genetic layout architecture, and data exchange. Prerequisites: CME104, CME106, CHEM 33, BIO41, BIO42, BIOE41, BIOE42, and BIOE44 (or equivalents), or permission of the instructors.

Regulatory approval and reimbursement for new health technologies are critical success factors for product commercialization. This course explores the regulatory and payer environment in the U.S. and abroad, as well as common methods of health technology assessment. Students will learn frameworks to identify factors relevant to the adoption of new health technologies, and the management of those factors in the design and development phases of bringing a product to market through case studies, guest speakers from government (FDA) and industry, and a course project.

Principles of tissue engineering and design strategies for practical applications for tissue repair. Topics include tissue morphogenesis, stem cells, biomaterials, controlled drug and gene delivery, and paper discussions. Students will learn skills for lab research through interactive lectures, paper discussions and research proposal development. Students work in small teams to work on develop research proposal for authentic tissue engineering problems. Lab sessions will teach techniques for culturing cells in 3D, as well as fabricating and characterizing hydrogels as 3D cell niche.

This course introduces computational modeling methods for cardiovascular blood flow and physiology. Topics in this course include analytical and computational methods for solutions of flow in deformable vessels, one-dimensional equations of blood flow, cardiovascular anatomy, lumped parameter models, vascular trees, scaling laws, biomechanics of the circulatory system, and 3D patient specific modeling with finite elements; course will provide an overview of the diagnosis and treatment of adult and congenital cardiovascular diseases and review recent research in the literature in a journal club format. Students will use SimVascular software to do clinically-oriented projects in patient specific blood flow simulations.

This course exposes students to the engineering principles and clinical application of medical devices through lectures and hands-on labs, performed in teams of two. Teams take measurements with these devices and fit their data to theory presented in the lecture. Devices covered include X-ray, CT, MRI, EEG, ECG, Ultrasound and BMI (Brain-machine interface). Prerequisites: BIOE 103 or BIOE 300B.

Principles of nuclear magnetic resonance relaxation theory as applicable to in vivo processes with an emphasis on medical imaging. Topics: physics and mathematics of relaxation, relaxation times in normal and diseased tissues, magnetization transfer contrast, chemical exchange saturation transfer, MRI contrast agents, and hyperpolarized 13C. Prerequisites: BIOE 22A

Combines biological knowledge and methods with quantitative engineering principles. Quantitative review of biochemistry and metabolism; recombinant DNA technology and synthetic biology (metabolic engineering). The production of protein pharaceuticals as a paradigm for the application of chemical engineering principles to advanced process development within the framework of current business and regulatory requirements. Prerequisite: CHEMENG 181 (formerly 188) or BIOSCI 41, or equivalent.

Materials design and engineering for regenerative medicine. How materials interact with cells through their micro- and nanostructure, mechanical properties, degradation characteristics, surface chemistry, and biochemistry. Examples include novel materials for drug and gene delivery, materials for stem cell proliferation and differentiation, and tissue engineering scaffolds. Prerequisites: undergraduate chemistry, and cell/molecular biology or biochemistry.

In this two-quarter course series ( BIOE 374A/B, MED 272A/B, ME 368A/B, OIT 384/5), multidisciplinary student teams identify real-world unmet healthcare needs, invent new health technologies to address them, and plan for their implementation into patient care. During the first quarter (winter), students select and characterize an important unmet healthcare problem, validate it through primary interviews and secondary research, and then brainstorm and screen initial technology-based solutions. In the second quarter (spring), teams select a lead solution and move it toward the market through prototyping, technical re-risking, strategies to address healthcare-specific requirements (regulation, reimbursement), and business planning. Final presentations in winter and spring are made to a panel of prominent health technology experts and/or investors. Class sessions include faculty-led instruction and case studies, coaching sessions by industry specialists, expert guest lecturers, and interactive team meetings. Enrollment is by application only, and students are expected to participate in both quarters of the course. Visit http://biodesign.stanford.edu/programs/stanford-courses/biodesign-innovation.html to access the application, examples of past projects, and student testimonials. More information about Stanford Biodesign, which has led to the creation of nearly 50 venture-backed healthcare companies and has helped hundreds of student launch health technology careers, can be found at http://biodesign.stanford.edu/.

May be used to prepare for research during a later quarter in 392. Faculty sponsor required. May be repeated for credit.

For Bioengineering graduate students. Previous work in 391 may be required for background; faculty sponsor required. May be repeated for credit.

Science and engineering researchers often spend days choosing a problem and years solving it. However, the problem initially chosen and subsequent course adjustments made along the project's decision tree, have an outsize influence on its likelihood of success and ultimate impact. This course will establish a framework for choosing problems and navigating a project's decision tree, emphasizing the role of intuition-building exercises and a stepwise analysis of assumptions. No prior knowledge is required.

Overview of cutting edge advances in biotechnology with a focus on therapeutic and health-related topics. Academic and industrial speakers from a range of areas including protein engineering, immuno-oncology, DNA sequencing, the microbiome, phamacogenomics, industrial enzymes, synthetic biology, and more. Course is designed for students interested in pursuing a career in the biotech industry

Principles for the design and optimization of new biological systems. Development of new enzymes, metabolic pathways, other metabolic systems, and communication systems among organisms. Example applications include the production of central metabolites, amino acids, pharmaceutical proteins, and isoprenoids. Economic challenges and quantitative assessment of metabolic performance. Pre- or corequisite: CHEMENG 355 or equivalent.

Students register through their affiliated department; otherwise register for CHEMENG 459. For specialists and non-specialists. Sponsored by the Stanford BioX Program. Three seminars per quarter address scientific and technical themes related to interdisciplinary approaches in bioengineering, medicine, and the chemical, physical, and biological sciences. Leading investigators from Stanford and the world present breakthroughs and endeavors that cut across core disciplines. Pre-seminars introduce basic concepts and background for non-experts. Registered students attend all pre-seminars; others welcome. See http://biox.stanford.edu/courses/459.html. Recommended: basic mathematics, biology, chemistry, and physics.

Direct experience with the computational tools used to create simulations of human movement. Lecture/labs on animation of movement; kinematic models of joints; forward dynamic simulation; computational models of muscles, tendons, and ligaments; creation of models from medical images; control of dynamic simulations; collision detection and contact models. Prerequisite: 281, 331A,B, or equivalent.

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