Explore Applied Quantitative Reasoning (AQR) WAYS Courses

Ways of Thinking/Ways of Doing

Title Requirements
AA 100
Introduction to Aeronautics and Astronautics
GER:DB-EngrAppSci, WAY-AQR, WAY-SMA

This class introduces the basics of aeronautics and astronautics through applied physics, hands-on activities, and real world examples. The principles of fluid flow, flight, and propulsion for aircraft will be illustrated, including the creation of lift and drag, aerodynamic performance including takeoff, climb, range, and landing. The principles of orbits, maneuvers, space environment, and propulsion for spacecraft will be illustrated. Students will be exposed to the history and challenges of aeronautics and astronautics.

AA 100
Introduction to Aeronautics and Astronautics
GER:DB-EngrAppSci, WAY-AQR, WAY-SMA

This class introduces the basics of aeronautics and astronautics through applied physics, hands-on activities, and real world examples. The principles of fluid flow, flight, and propulsion for aircraft will be illustrated, including the creation of lift and drag, aerodynamic performance including takeoff, climb, range, and landing. The principles of orbits, maneuvers, space environment, and propulsion for spacecraft will be illustrated. Students will be exposed to the history and challenges of aeronautics and astronautics.

AA 100
Introduction to Aeronautics and Astronautics
GER:DB-EngrAppSci, WAY-AQR, WAY-SMA

This class introduces the basics of aeronautics and astronautics through applied physics, hands-on activities, and real world examples. The principles of fluid flow, flight, and propulsion for aircraft will be illustrated, including the creation of lift and drag, aerodynamic performance including takeoff, climb, range, and landing. The principles of orbits, maneuvers, space environment, and propulsion for spacecraft will be illustrated. Students will be exposed to the history and challenges of aeronautics and astronautics.

AA 109Q
Aerodynamics of Race Cars
WAY-AQR

Almost as soon as cars had been invented, races of various kinds were organized. In all its forms (open-wheel, touring car, sports car, production-car, one-make, stock car, etc.), car racing is today a very popular sport with a huge media coverage and significant commercial sponsorships. More importantly, it is a proving ground for new technologies and a battlefield for the giants of the automotive industry. While race car performance depends on elements such as engine power, chassis design, tire adhesion and of course, the driver, aerodynamics probably plays the most vital role in determining the performance and efficiency of a race car. Front and/or rear wings are visible on many of them. During this seminar, you will learn about many other critical components of a race car including diffusers and add-ons such as vortex generators and spoilers. You will also discover that due to the competitive nature of this sport and its associated short design cycles, engineering decisions about a race car must rely on combined information from track, wind tunnel, and numerical computations. It is clear that airplanes fly on wings. However, when you have completed this seminar, you will be able to understand that cars fly on their tires. You will also be able to appreciate that aerodynamics is important not only for drag reduction, but also for increasing cornering speeds and lateral stability. You will be able to correlate between a race car shape and the aerodynamics effects intended for influencing performance. And if you have been a fan of the Ferrari 458 Italia, you will be able to figure out what that black moustache in the front of the car was for.

AA 109Q
Aerodynamics of Race Cars
WAY-AQR

Almost as soon as cars had been invented, races of various kinds were organized. In all its forms (open-wheel, touring car, sports car, production-car, one-make, stock car, etc.), car racing is today a very popular sport with a huge media coverage and significant commercial sponsorships. More importantly, it is a proving ground for new technologies and a battlefield for the giants of the automotive industry. While race car performance depends on elements such as engine power, chassis design, tire adhesion and of course, the driver, aerodynamics probably plays the most vital role in determining the performance and efficiency of a race car. Front and/or rear wings are visible on many of them. During this seminar, you will learn about many other critical components of a race car including diffusers and add-ons such as vortex generators and spoilers. You will also discover that due to the competitive nature of this sport and its associated short design cycles, engineering decisions about a race car must rely on combined information from track, wind tunnel, and numerical computations. It is clear that airplanes fly on wings. However, when you have completed this seminar, you will be able to understand that cars fly on their tires. You will also be able to appreciate that aerodynamics is important not only for drag reduction, but also for increasing cornering speeds and lateral stability. You will be able to correlate between a race car shape and the aerodynamics effects intended for influencing performance. And if you have been a fan of the Ferrari 458 Italia, you will be able to figure out what that black moustache in the front of the car was for.

AA 115N
The Global Positioning System: Where on Earth are We, and What Time is It?
GER:DB-EngrAppSci, WAY-AQR

Preference to freshmen. Why people want to know where they are: answers include cross-Pacific trips of Polynesians, missile guidance, and distraught callers. How people determine where they are: navigation technology from dead-reckoning, sextants, and satellite navigation (GPS). Hands-on experience. How GPS works; when it does not work; possibilities for improving performance.

AA 115N
The Global Positioning System: Where on Earth are We, and What Time is It?
GER:DB-EngrAppSci, WAY-AQR

Preference to freshmen. Why people want to know where they are: answers include cross-Pacific trips of Polynesians, missile guidance, and distraught callers. How people determine where they are: navigation technology from dead-reckoning, sextants, and satellite navigation (GPS). Hands-on experience. How GPS works; when it does not work; possibilities for improving performance.

AA 115Q
The Global Positioning System: Where on Earth are We, and What Time is It?
GER:DB-EngrAppSci, WAY-AQR

Preference to freshmen. Why people want to know where they are: answers include cross-Pacific trips of Polynesians, missile guidance, and distraught callers. How people determine where they are: navigation technology from dead-reckoning, sextants, and satellite navigation (GPS). Hands-on experience. How GPS works; when it does not work; possibilities for improving performance.

AA 118N
How to Design a Space Mission: from Concept to Execution
WAY-AQR, WAY-SMA

Space exploration is truly fascinating. From the space race led by governments as an outgrowth of the Cold War to the new era of space commercialization led by private companies and startups, more than 50 years have passed, characterized by great leaps forward and discoveries. We will learn how space missions are designed, from concept to execution, based on the professional experience of the lecturer and numerous examples of spacecraft, including unique hardware demonstrations by startups of the Silicon Valley. We will study the essentials of systems engineering as applicable to a variety of mission types, for communication, navigation, science, commercial, and military applications. We will explore the various elements of a space mission, including the spacecraft, ground, and launch segments with their functionalities. Special emphasis will be given to the design cycle, to understand how spacecraft are born, from the stakeholders' needs, through analysis, synthesis, all the way to their integration and validation. We will compare the current designs with those employed in the early days of the space age, and show the importance of economics in the development of spacecraft. Finally, we will brainstorm startup ideas and apply the concepts learned to a notional space mission design as a team.

AA 118N
How to Design a Space Mission: from Concept to Execution
WAY-AQR, WAY-SMA

Space exploration is truly fascinating. From the space race led by governments as an outgrowth of the Cold War to the new era of space commercialization led by private companies and startups, more than 50 years have passed, characterized by great leaps forward and discoveries. We will learn how space missions are designed, from concept to execution, based on the professional experience of the lecturer and numerous examples of spacecraft, including unique hardware demonstrations by startups of the Silicon Valley. We will study the essentials of systems engineering as applicable to a variety of mission types, for communication, navigation, science, commercial, and military applications. We will explore the various elements of a space mission, including the spacecraft, ground, and launch segments with their functionalities. Special emphasis will be given to the design cycle, to understand how spacecraft are born, from the stakeholders' needs, through analysis, synthesis, all the way to their integration and validation. We will compare the current designs with those employed in the early days of the space age, and show the importance of economics in the development of spacecraft. Finally, we will brainstorm startup ideas and apply the concepts learned to a notional space mission design as a team.

AA 118N
How to Design a Space Mission: from Concept to Execution
WAY-AQR, WAY-SMA

Space exploration is truly fascinating. From the space race led by governments as an outgrowth of the Cold War to the new era of space commercialization led by private companies and startups, more than 50 years have passed, characterized by great leaps forward and discoveries. We will learn how space missions are designed, from concept to execution, based on the professional experience of the lecturer and numerous examples of spacecraft, including unique hardware demonstrations by startups of the Silicon Valley. We will study the essentials of systems engineering as applicable to a variety of mission types, for communication, navigation, science, commercial, and military applications. We will explore the various elements of a space mission, including the spacecraft, ground, and launch segments with their functionalities. Special emphasis will be given to the design cycle, to understand how spacecraft are born, from the stakeholders' needs, through analysis, synthesis, all the way to their integration and validation. We will compare the current designs with those employed in the early days of the space age, and show the importance of economics in the development of spacecraft. Finally, we will brainstorm startup ideas and apply the concepts learned to a notional space mission design as a team.

AA 119N
3D Printed Aerospace Structures
WAY-AQR

The demand for rapid prototyping of lightweight, complex, and low-cost structures has led the aerospace industry to leverage three-dimensional (3D) printing as a manufacturing technology. For example, the manufacture of aircraft engine components, unmanned aerial vehicle (UAV) wings, CubeSat parts, and satellite sub-systems have recently been realized with 3D printing and other additive manufacturing techniques. In this freshman seminar, a survey of state-of-the-art 3D printing processes will be reviewed and the process-dependent properties of 3D-printed materials and structures will be analyzed in detail. In addition, the advantages and disadvantages of this manufacturing approach will be debated during class! To give students exposure to 3D printing systems in action, tours of actual 3D printing facilities on campus (Stanford's Product Realization Laboratory), as well as in Silicon Valley (e.g., Made in Space) will be conducted.

AA 120Q
Building Trust in Autonomy
WAY-AQR, WAY-SMA

Major advances in both hardware and software have accelerated the development of autonomous systems that have the potential to bring significant benefits to society. Google, Tesla, and a host of other companies are building autonomous vehicles that can improve safety and provide flexible mobility options for those who cannot drive themselves. On the aviation side, the past few years have seen the proliferation of unmanned aircraft that have the potential to deliver medicine and monitor agricultural crops autonomously. In the financial domain, a significant portion of stock trades are performed using automated trading algorithms at a frequency not possible by human traders. How do we build these systems that drive our cars, fly our planes, and invest our money? How do we develop trust in these systems? What is the societal impact on increased levels of autonomy?

AA 121Q
It IS Rocket Science!
WAY-AQR, WAY-SMA

It's an exciting time for space exploration. Companies like SpaceX and Blue Origin are launching rockets into space and bringing them back for reuse. NASA is developing the world's most powerful rocket. Startups are deploying constellations of hundreds of cubesats for communications, navigation, and earth monitoring. The human race has recently gotten a close look at Pluto, soft landed on a comet, and orbited two asteroids. The upcoming launch of the James Webb Space Telescope will allow astronomers to look closer to the beginning of time than ever before. The workings of space systems remain mysterious to most people, but in this seminar we'll pull back the curtain for a look at the basics of "rocket science." How does a SpaceX rocket get into space? How do Skybox satellites capture images for Google Earth? How did the New Horizons probe find its way to Pluto? How do we communicate with spacecraft that are so distant? We'll explore these topics and a range of others during the quarter. We'll cover just enough physics and math to determine where to look in the sky for a spacecraft, planet, or star. Then we'll check our math by going outside for an evening pizza party observing these objects in the night sky. We'll also visit a spacecraft production facility or Mission Operations Center to see theory put into practice.

AA 122N
Dawn of the Drones: How Will Unmanned Aerial Systems Change Our World?
WAY-AQR, WAY-SMA

Unmanned aerial systems (UASs) have exploded on the scene in recent years, igniting a national debate about how to use them, how to regulate them, and how to make them safe. This seminar will dive into the many engineering challenges behind the headlines: in the future, how will we engineer UASs ranging in size from simple RC toys to highly-sophisticated autonomous scientific and military data gathering systems? This seminar will examine the key elements required to conceive, implement, deploy, and operate state-of-the-art of drone systems: What variety of problems can they help us solve? How autonomous are they and how autonomous do they need to be? What are the key technical bottlenecks preventing widespread deployment? How are they different from commercial aircraft? What kinds of companies will serve the market for UAV-related products and services? What business models will be successful and why? We will emphasize aspects of design, autonomy, reliability, navigation, sensing, and perception, as well as coordination/collaboration through a series of case studies drawn from our recent experience. Examples include imaging efforts to map the changing coral reefs in the South Pacific, using and controlling swarms of unmanned systems to perform search and rescue missions over large areas, and package delivery systems over large metropolitan areas. Hands-on experience with Stanford-developed UASs will be part of the seminar.

AA 131
Space Flight
WAY-AQR

This class is all about how to build a spacecraft. It is designed to introduce undergraduate engineering students to the engineering fundamentals of conceiving, designing, implementing, and operating satellites and other space systems. Topics include orbital dynamics, attitude dynamics, mission design, and subsystem technologies. The space environment and the seven classic spacecraft subsystems - propulsion, attitude control and navigation, structure, thermal, power, telemetry and command, and payload - will be explored in detail. Prerequisites: Freshman-level physics, basic calculus and differential equations.

AA 136B
Spacecraft Design Laboratory (AA 236B)
WAY-AQR

Space Capstone II. Required for Aero/Astro majors. Continuation of 236A. Emphasis is on practical application of systems engineering to the life cycle program of spacecraft design, testing, launching, and operations. Prerequisite: 236A or consent of instructor.

ANTHRO 116
Data Analysis for Quantitative Research (ANTHRO 216)
GER:DB-SocSci, WAY-AQR

An introduction to numeric methods in Anthropology and related fields employing the Data Desk statistics package to test hypotheses and to explore data. Examples chosen from the instructor¿s research and other relevant projects. No statistical background is necessary, but a working knowledge of algebra is important. Topics covered include: Frequency Distributions; Measures of Central Tendency, Dispersion, and Variability; Probability and Probability Distributions; Statistical Inference, Comparisons of Sample Means and Standard Deviations; Analysis of Variance; Contingency Tables, Comparisons of Frequencies; Correlation and Regression; Principal Components Analysis; Discriminant Analysis; and Cluster Analysis. Grading based on take-home problem sets.

ANTHRO 116
Data Analysis for Quantitative Research (ANTHRO 216)
GER:DB-SocSci, WAY-AQR

An introduction to numeric methods in Anthropology and related fields employing the Data Desk statistics package to test hypotheses and to explore data. Examples chosen from the instructor¿s research and other relevant projects. No statistical background is necessary, but a working knowledge of algebra is important. Topics covered include: Frequency Distributions; Measures of Central Tendency, Dispersion, and Variability; Probability and Probability Distributions; Statistical Inference, Comparisons of Sample Means and Standard Deviations; Analysis of Variance; Contingency Tables, Comparisons of Frequencies; Correlation and Regression; Principal Components Analysis; Discriminant Analysis; and Cluster Analysis. Grading based on take-home problem sets.

ANTHRO 130D
Spatial Approaches to Social Science (ANTHRO 230D, POLISCI 241S, URBANST 124)
WAY-AQR, WAY-SI

This multidisciplinary course combines different approaches to how GIS and spatial tools can be applied in social science research. We take a collaborative, project oriented approach to bring together technical expertise and substantive applications from several social science disciplines. The course aims to integrate tools, methods, and current debates in social science research and will enable students to engage in critical spatial research and a multidisciplinary dialogue around geographic space.

ANTHRO 130D
Spatial Approaches to Social Science (ANTHRO 230D, POLISCI 241S, URBANST 124)
WAY-AQR, WAY-SI

This multidisciplinary course combines different approaches to how GIS and spatial tools can be applied in social science research. We take a collaborative, project oriented approach to bring together technical expertise and substantive applications from several social science disciplines. The course aims to integrate tools, methods, and current debates in social science research and will enable students to engage in critical spatial research and a multidisciplinary dialogue around geographic space.

APPPHYS 189
Physical Analysis of Artworks
WAY-AQR, WAY-SMA

Students explore the use of Stanford Nano Shared Facilities (SNSF) for physical analysis of material samples of interest for art conservation, technical art history and archaeology. Weekly SNSF demonstrations will be supplemented by lectures on intellectual context by Stanford faculty/staff and conservators from the Fine Arts Museums of San Francisco (FAMSF). Students will complete the SNSF training sequence for electron microscopy and undertake analysis projects derived from ongoing conservation efforts at FAMSF."

APPPHYS 61
Science as a Creative Process (BIO 61)
WAY-AQR, WAY-SMA

What is the process of science, and why does creativity matter? We'll delve deeply into the applicability of science in addressing a vast range of real-world problems. This course is designed to teach the scientific method as it's actually practiced by working scientists. It will cover how to ask a well-posed question, how to design a good experiment, how to collect and interpret quantitative data, how to recover from error, and how to communicate findings. Facts matter! Course topics will include experimental design, statistics and statistical significance, formulating appropriate controls, modeling, peer review, and more. The course will incorporate a significant hands-on component featuring device fabrication, testing, and measurement. Among other "Dorm Science" activities, we'll be distributing Arduino microcontroller kits and electronic sensors, then use these items, along with other materials, to complete a variety of group and individual projects outside the classroom. The final course assignment will be to develop and write a scientific grant proposal to test a student-selected myth or scientific controversy. Although helpful, no prior experience with electronics or computer programming is required. Recommended for freshmen.

APPPHYS 61
Science as a Creative Process (BIO 61)
WAY-AQR, WAY-SMA

What is the process of science, and why does creativity matter? We'll delve deeply into the applicability of science in addressing a vast range of real-world problems. This course is designed to teach the scientific method as it's actually practiced by working scientists. It will cover how to ask a well-posed question, how to design a good experiment, how to collect and interpret quantitative data, how to recover from error, and how to communicate findings. Facts matter! Course topics will include experimental design, statistics and statistical significance, formulating appropriate controls, modeling, peer review, and more. The course will incorporate a significant hands-on component featuring device fabrication, testing, and measurement. Among other "Dorm Science" activities, we'll be distributing Arduino microcontroller kits and electronic sensors, then use these items, along with other materials, to complete a variety of group and individual projects outside the classroom. The final course assignment will be to develop and write a scientific grant proposal to test a student-selected myth or scientific controversy. Although helpful, no prior experience with electronics or computer programming is required. Recommended for freshmen.

BIO 141
Biostatistics (STATS 141)
GER:DB-Math, WAY-AQR

Introductory statistical methods for biological data: describing data (numerical and graphical summaries); introduction to probability; and statistical inference (hypothesis tests and confidence intervals). Intermediate statistical methods: comparing groups (analysis of variance); analyzing associations (linear and logistic regression); and methods for categorical data (contingency tables and odds ratio). Course content integrated with statistical computing in R.

BIO 141
Biostatistics (STATS 141)
GER:DB-Math, WAY-AQR

Introductory statistical methods for biological data: describing data (numerical and graphical summaries); introduction to probability; and statistical inference (hypothesis tests and confidence intervals). Intermediate statistical methods: comparing groups (analysis of variance); analyzing associations (linear and logistic regression); and methods for categorical data (contingency tables and odds ratio). Course content integrated with statistical computing in R.

BIO 141
Biostatistics (STATS 141)
GER:DB-Math, WAY-AQR

Introductory statistical methods for biological data: describing data (numerical and graphical summaries); introduction to probability; and statistical inference (hypothesis tests and confidence intervals). Intermediate statistical methods: comparing groups (analysis of variance); analyzing associations (linear and logistic regression); and methods for categorical data (contingency tables and odds ratio). Course content integrated with statistical computing in R.

BIO 183
Theoretical Population Genetics (BIO 283)
WAY-AQR, WAY-SMA

Models in population genetics and evolution. Selection, random drift, gene linkage, migration, and inbreeding, and their influence on the evolution of gene frequencies and chromosome structure. Models are related to DNA sequence evolution. Prerequisites: calculus and linear algebra, or consent of instructor.

BIO 183
Theoretical Population Genetics (BIO 283)
WAY-AQR, WAY-SMA

Models in population genetics and evolution. Selection, random drift, gene linkage, migration, and inbreeding, and their influence on the evolution of gene frequencies and chromosome structure. Models are related to DNA sequence evolution. Prerequisites: calculus and linear algebra, or consent of instructor.

BIO 61
Science as a Creative Process (APPPHYS 61)
WAY-AQR, WAY-SMA

What is the process of science, and why does creativity matter? We'll delve deeply into the applicability of science in addressing a vast range of real-world problems. This course is designed to teach the scientific method as it's actually practiced by working scientists. It will cover how to ask a well-posed question, how to design a good experiment, how to collect and interpret quantitative data, how to recover from error, and how to communicate findings. Facts matter! Course topics will include experimental design, statistics and statistical significance, formulating appropriate controls, modeling, peer review, and more. The course will incorporate a significant hands-on component featuring device fabrication, testing, and measurement. Among other "Dorm Science" activities, we'll be distributing Arduino microcontroller kits and electronic sensors, then use these items, along with other materials, to complete a variety of group and individual projects outside the classroom. The final course assignment will be to develop and write a scientific grant proposal to test a student-selected myth or scientific controversy. Although helpful, no prior experience with electronics or computer programming is required. Recommended for freshmen.

BIO 61
Science as a Creative Process (APPPHYS 61)
WAY-AQR, WAY-SMA

What is the process of science, and why does creativity matter? We'll delve deeply into the applicability of science in addressing a vast range of real-world problems. This course is designed to teach the scientific method as it's actually practiced by working scientists. It will cover how to ask a well-posed question, how to design a good experiment, how to collect and interpret quantitative data, how to recover from error, and how to communicate findings. Facts matter! Course topics will include experimental design, statistics and statistical significance, formulating appropriate controls, modeling, peer review, and more. The course will incorporate a significant hands-on component featuring device fabrication, testing, and measurement. Among other "Dorm Science" activities, we'll be distributing Arduino microcontroller kits and electronic sensors, then use these items, along with other materials, to complete a variety of group and individual projects outside the classroom. The final course assignment will be to develop and write a scientific grant proposal to test a student-selected myth or scientific controversy. Although helpful, no prior experience with electronics or computer programming is required. Recommended for freshmen.

BIO 61
Science as a Creative Process (APPPHYS 61)
WAY-AQR, WAY-SMA

What is the process of science, and why does creativity matter? We'll delve deeply into the applicability of science in addressing a vast range of real-world problems. This course is designed to teach the scientific method as it's actually practiced by working scientists. It will cover how to ask a well-posed question, how to design a good experiment, how to collect and interpret quantitative data, how to recover from error, and how to communicate findings. Facts matter! Course topics will include experimental design, statistics and statistical significance, formulating appropriate controls, modeling, peer review, and more. The course will incorporate a significant hands-on component featuring device fabrication, testing, and measurement. Among other "Dorm Science" activities, we'll be distributing Arduino microcontroller kits and electronic sensors, then use these items, along with other materials, to complete a variety of group and individual projects outside the classroom. The final course assignment will be to develop and write a scientific grant proposal to test a student-selected myth or scientific controversy. Although helpful, no prior experience with electronics or computer programming is required. Recommended for freshmen.

BIODS 48N
Riding the Data Wave (STATS 48N)
WAY-AQR, WAY-FR

Imagine collecting a bit of your saliva and sending it in to one of the personalized genomics company: for very little money you will get back information about hundreds of thousands of variable sites in your genome. Records of exposure to a variety of chemicals in the areas you have lived are only a few clicks away on the web; as are thousands of studies and informal reports on the effects of different diets, to which you can compare your own. What does this all mean for you? Never before in history humans have recorded so much information about themselves and the world that surrounds them. Nor has this data been so readily available to the lay person. Expression as "data deluge'' are used to describe such wealth as well as the loss of proper bearings that it often generates. How to summarize all this information in a useful way? How to boil down millions of numbers to just a meaningful few? How to convey the gist of the story in a picture without misleading oversimplifications? To answer these questions we need to consider the use of the data, appreciate the diversity that they represent, and understand how people instinctively interpret numbers and pictures. During each week, we will consider a different data set to be summarized with a different goal. We will review analysis of similar problems carried out in the past and explore if and how the same tools can be useful today. We will pay attention to contemporary media (newspapers, blogs, etc.) to identify settings similar to the ones we are examining and critique the displays and summaries there documented. Taking an experimental approach, we will evaluate the effectiveness of different data summaries in conveying the desired information by testing them on subsets of the enrolled students.

BIOE 101
Systems Biology (BIOE 210)
WAY-AQR

Complex biological behaviors through the integration of computational modeling and molecular biology. Topics: reconstructing biological networks from high-throughput data and knowledge bases. Network properties. Computational modeling of network behaviors at the small and large scale. Using model predictions to guide an experimental program. Robustness, noise, and cellular variation. Prerequisites: CME 102; BIO 82, BIO 84; or consent of instructor.

BIOE 101
Systems Biology (BIOE 210)
WAY-AQR

Complex biological behaviors through the integration of computational modeling and molecular biology. Topics: reconstructing biological networks from high-throughput data and knowledge bases. Network properties. Computational modeling of network behaviors at the small and large scale. Using model predictions to guide an experimental program. Robustness, noise, and cellular variation. Prerequisites: CME 102; BIO 82, BIO 84; or consent of instructor.

BIOE 101
Systems Biology (BIOE 210)
WAY-AQR

Complex biological behaviors through the integration of computational modeling and molecular biology. Topics: reconstructing biological networks from high-throughput data and knowledge bases. Network properties. Computational modeling of network behaviors at the small and large scale. Using model predictions to guide an experimental program. Robustness, noise, and cellular variation. Prerequisites: CME 102; BIO 82, BIO 84; or consent of instructor.

BIOE 102
Physical Biology of Macromolecules
WAY-AQR, WAY-SMA

Principles of statistical physics, thermodynamics, and kinetics with applications to molecular biology. Topics include entropy, temperature, chemical forces, enzyme kinetics, free energy and its uses, self assembly, cooperative transitions in macromolecules, molecular machines, feedback, and accurate replication. Prerequisites: MATH 19, 20, 21; CHEM 31A, B (or 31X); strongly recommended: PHYSICS 41, CME 100 or MATH 51, and CME 106; or instructor approval.

BIOE 103
Systems Physiology and Design
WAY-AQR, WAY-SMA

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.

BIOE 103
Systems Physiology and Design
WAY-AQR, WAY-SMA

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.

BIOE 103
Systems Physiology and Design
WAY-AQR, WAY-SMA

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.

BIOE 103B
Systems Physiology and Design
WAY-AQR, WAY-SMA

*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

BIOE 103B
Systems Physiology and Design
WAY-AQR, WAY-SMA

*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

BIOE 103B
Systems Physiology and Design
WAY-AQR, WAY-SMA

*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

BIOE 158
Soft Matter in Biomedical Devices, Microelectronics, and Everyday Life (CHEMENG 160, MATSCI 158)
WAY-AQR, WAY-SMA

The relationships between molecular structure, morphology, and the unique physical, chemical, and mechanical behavior of polymers and other types of soft matter are discussed. Topics include methods for preparing synthetic polymers and examination of how enthalpy and entropy determine conformation, solubility, mechanical behavior, microphase separation, crystallinity, glass transitions, elasticity, and linear viscoelasticity. Case studies covering polymers in biomedical devices and microelectronics will be covered. Recommended: ENGR 50 and Chem 31A or equivalent.

BIOE 158
Soft Matter in Biomedical Devices, Microelectronics, and Everyday Life (MATSCI 158)
WAY-AQR, WAY-SMA

The relationships between molecular structure, morphology, and the unique physical, chemical, and mechanical behavior of polymers and other types of soft matter are discussed. Topics include methods for preparing synthetic polymers and examination of how enthalpy and entropy determine conformation, solubility, mechanical behavior, microphase separation, crystallinity, glass transitions, elasticity, and linear viscoelasticity. Case studies covering polymers in biomedical devices and microelectronics will be covered. Recommended: ENGR 50 and Chem 31A or equivalent.

BIOE 42
Physical Biology
WAY-AQR, WAY-SMA

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.

BIOE 42
Physical Biology
WAY-AQR, WAY-SMA

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.

BIOE 42
Physical Biology
WAY-AQR, WAY-SMA

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.

BIOHOPK 14
Bio-logging and Bio-telemetry
WAY-AQR, WAY-SMA

Bio-logging is a rapidly growing discipline that includes diverse fields such as consumer electronics, medicine, and marine biology. The use of animal-attached digital tags is a powerful approach to study the movement and ecology of individuals over a wide range of temporal and spatial scales. This course is an introduction to bio-logging methods and analysis. Using whales as a model system, students will learn how use multi-sensor tags to study behavioral biomechanics.

BIOHOPK 174H
Experimental Design and Probability (BIOHOPK 274H)
GER: DB-NatSci, GER:DB-Math, WAY-AQR, WAY-FR

(Graduate students register for 274H.) Variability is an integral part of biology. Introduction to probability and its use in designing experiments to address biological problems. Focus is on analysis of variance, when and how to use it, why it works, and how to interpret the results. Design of complex, but practical, asymmetrical experiments and environmental impact studies, and regression and analysis of covariance. Computer-based data analysis. Prerequisite: Biology core or consent of instructor.

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