Objectives & Outcomes

Student Learning Outcomes: The goal is for undergraduate engineering students to gain sufficient biology and human physiology fundamentals so that they are better prepared to study specialized topics, e.g., biomechanics, imaging, computational biology, tissue engineering, biomonitoring, drug development, robotics, and other topics covered by upper division and graduate courses in UC Berkeley departments of Molecular and Cell Biology, Integrative Biology, Bioengineering, Electrical Engineering and Computer Science, Mechanical Engineering, and courses in the UC San Francisco Division of Bioengineering.

Rules & Requirements

Prerequisites: MATH 1A or MATH 16A or another introductory calculus course (can be taken concurrently)

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructors: Conboy, Kumar, Johnson

Objectives & Outcomes

Course Objectives: The goal of this course is to give students the background in organic chemistry and biochemistry needed understand problems in synthetic biology, biomaterials and molecular imaging. Emphasis is on basic mechanisms

Student Learning Outcomes: Students will learn aspects of organic and biochemistry required to begin the rational manipulation and/or design of biological systems and the molecules they are comprised of.

Rules & Requirements

Prerequisites: CHEM 3A

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Rules & Requirements

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1 hour of seminar per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Offered for pass/not pass grade only. Final Exam To be decided by the instructor when the class is offered.

Rules & Requirements

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1 hour of seminar per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

Objectives & Outcomes

Course Objectives: This course is designed to expose students to current research and problems in bioengineering. As a freshman/sophomore class, its main purpose is to excite our students about the possibilities of bioengineering and to help them to choose an area of focus.

Student Learning Outcomes: This course demonstrates the rapid pace of new technology and the need for life-long learning (2). In addition, the course, because of its state-of-the-art research content, encourages our students to explore new horizons (3).

Hours & Format

Fall and/or spring: 15 weeks - 1 hour of seminar per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

Instructors: T. Johnson, H. Lam

Rules & Requirements

Prerequisites: Consent of instructor

Credit Restrictions: Enrollment is restricted; see the Introduction to Courses and Curricul a section of this catalog.

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1-4 hours of directed group study per week

Summer: 8 weeks - 1-4 hours of directed group study per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

Rules & Requirements

Prerequisites: Freshman or sophomore standing and consent of instructor

Credit Restrictions: Enrollment is restricted; see the Introduction to Courses and Curricula section of this catalog.

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1-4 hours of independent study per week

Summer:
8 weeks - 1.5-7.5 hours of independent study per week
10 weeks - 1.5-6 hours of independent study per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructors: Lam, Hayley

Objectives & Outcomes

Course Objectives: Students should understand the architecture and design principles of modern biomedical sensor data-acquisition (sensor-DAQ) systems. They should understand how to choose the appropriate biomedical sensor, instrumentation amplifier, number of bits, sampling rate, anti-aliasing filter, and DAQ system. They will learn how to design a low-noise instrumentation amplifier circuit. They should understand the crucial importance of suppressing 60 Hz and other interferences to acquire high quality low-level biomedical signals. They should understand the design principles of building, debugging.

Student Learning Outcomes: Students will achieve knowledge and skills in biomedical signal acquisition. They will be assessed in their success with the Course Objectives through tests, homeworks, and laboratories. In particular, the tests will ensure that the students have absorbed the theoretical concepts. The laboratories will provide assessment of learning practical skills (e.g., building an ECG circuit).

Rules & Requirements

Prerequisites: EECS 16A, EECS 16B, MATH 53, MATH 54, PHYSICS 7A, and PHYSICS 7B; or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Conolly

Objectives & Outcomes

Course Objectives: This course introduces, develops and applies scaling laws and the methods of continuum mechanics to biomechanical phenomena related to tissue or organ levels. It is intended for upper level undergraduate students who have been exposed to vectors, differential equations, and undergraduate course(s) in physics and certain aspects of modern biology.
Topics include:
•
Biosolid mechanics
•
Stress, strain, constitutive equation
•
Vector and tensor math
•
Equilibrium
•
Extension, torsion, bending, buckling
•
Material properties of tissues

Student Learning Outcomes: The course will equip the students with a deep understanding of principles of biomechanics. The intuitions gained in this course will help guide the analysis of design of biomedical devices and help the understanding of biological/medical phenomena in health and disease.
The students will develop insight, skills and tools in quantitative analysis of diverse biomechanical systems and topics, spanning various scales from cellular to tissue and organ levels.

Rules & Requirements

Prerequisites: MATH 53, MATH 54, and PHYSICS 7A

Credit Restrictions: Students will receive no credit for BIO ENG 102 after completing MEC ENG C85.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Mofrad

Objectives & Outcomes

Course Objectives: (1) To introduce the basics of thermodynamics and chemical kinetics for molecular to cellular biological systems; (2) To give students an understanding of biological size and timescales illustrated through computational exercises on model problems in physical biology.

Student Learning Outcomes: students will be able to (1) relate statistical thermodynamics and chemical kinetics to analyze molecular and cellular behavior beyond the ideal gas and Carnot cycle.

Rules & Requirements

Prerequisites: PHYSICS 7A, PHYSICS 7B, MATH 1A, MATH 1B, MATH 53, and MATH 54; and BIOLOGY 1A or BIO ENG 11

Credit Restrictions: Students will receive no credit for Bioengineering 103 after completing Chemistry 120B, or Molecular Cell Biology C100A/Chemistry C130.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Head-Gordon

Rules & Requirements

Prerequisites: MATH 53, MATH 54, and PHYSICS 7A

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Johnson

Objectives & Outcomes

Course Objectives: ● To prepare students to engage in upper division device design work
● Establish a foundational understanding of biomedical device electronics, signal acquisition, sampling, and reconstruction
● To learn quantitative approaches to analyze biomedical signals
● Reinforce mathematical principles including linear algebra, differential equations
● Establish proficiency in the use of MATLAB as a tool for analyzing biomedical data

Student Learning Outcomes: To give students the mathematical and physical tools required to engage in device design.

Rules & Requirements

Prerequisites: MATH 53, PHYSICS 7A, and PHYSICS 7B

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Moriel Vandsburger

Rules & Requirements

Prerequisites: Familiarity with linear algebra at the level of EECS 16A/EECS 16B or Math 54. Experience coding in python at the level of COMPSCI 61A. Preferred: experience developing software at the level of COMPSCI 61B and experience using Linux

Credit Restrictions: Students will receive no credit for Electrical Engineering and Computer Science C106A/Bioengineering C106A after completing EE C106A/BioE C125, Electrical Engineering 206A, or Electrical Engineering and Computer Science 206A.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 3 hours of laboratory per week

Summer: 8 weeks - 6 hours of lecture, 2 hours of discussion, and 6 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Sastry

Also listed as: EECS C106A/MEC ENG C106A

Rules & Requirements

Prerequisites: EECS C106A / BIO ENG C106A / MEC ENG C106A / EECS C206A or an equivalent course. A strong programming background, knowledge of Python and Matlab, and some coursework in feedback controls (such as EL ENG C128 / MEC ENG C134) are also useful. Students who have not taken the prerequisite course should have a strong programming background, knowledge of Python and Matlab, and exposure to linear algebra, Lagrangian dynamics, and feedback controls at the intermediate level. EECS C106A

Credit Restrictions: Students will receive no credit for Electrical Engineering and Computer Science C106B/Bioengineering C106B after completing Electrical Engineering C106B/Bioengineering C125B, Electrical Engineering 206B, or Electrical Engineering and Computer Science 206B.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Sastry

Also listed as: EECS C106B/MEC ENG C106B

Objectives & Outcomes

Course Objectives: This 15-week course will introduce students to the principles of medical physiology, with a strong emphasis on quantitative problem solving, the physiological basis of human disease, and applications to biomedical devices and prostheses.

Student Learning Outcomes: Students will be exposed to the basic physiological systems which govern the function of each organ system, examples of diseases in which these systems go awry, and medical devices which have been developed to correct the deficits.

Rules & Requirements

Prerequisites: BIO ENG 10; and BIO ENG 11 or BIOLOGY 1A; and MATH 54 recommended

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Kumar

Objectives & Outcomes

Course Objectives: To provide students with basic and extended concepts for the development of the functional proteins and their characterization for various bioengineering and biomedical purposes.

Student Learning Outcomes: Upon completing the course, the student should be able:
1.
To understand the directed evolution processes of functional proteins.
2.
To identify the natural protein products from proteomic database.
3.
To design various experiments to characterize the new protein products.
4.
To develop novel functional proteins and characterize their properties.
5.
To understand basic concepts and instrumentation of protein characterization tools.

Rules & Requirements

Prerequisites: CHEM 1A or CHEM 4A; BIO ENG 11 or BIOLOGY 1A; and BIO ENG 103

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: SW Lee

Objectives & Outcomes

Course Objectives: This course, which is open to senior undergraduate students or graduate students in diverse disciplines ranging from engineering to biology to chemistry and physics, is aimed at exposing students to subcellular biomechanical phenomena spanning scales from molecules to the whole cell.

Student Learning Outcomes: The students will develop tools and skills to (1) understand and analyze subcelluar biomechanics and transport phenomena, and (2) ultimately apply these skills to novel biological and biomedical applications

Rules & Requirements

Prerequisites: BIO ENG 102; or MEC ENG C85 / CIV ENG C30; or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Mofrad

Also listed as: MEC ENG C115

Objectives & Outcomes

Course Objectives: The goal of this course to establish fundamental understanding of cell engineering technologies and of the key biological paradigms, upon which cell engineering is based, with the focus on biomedical applications of cell engineering.

Student Learning Outcomes: At the completion of this course students will understand how bioengineering technologies address the deliberate control of cell properties (and how this advances biomedicine); and students will learn the main concepts and current views on key attributes of animal cells (somatic, embryonic, pluripotent, germ-line; with the focus on mammalian cells).

Rules & Requirements

Prerequisites: BIOLOGY 1A or BIO ENG 11; or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 2 hours of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Conboy

Objectives & Outcomes

Course Objectives: The goal of this course to provide students with conceptual and practical understanding of cell and tissue bioengineering.

Student Learning Outcomes: At the completion of this course, students will learn key cellular bioengineering laboratory techniques, will develop a conceptual and theoretical understanding of the reliability and limitations of these techniques and will enhance their skills in quantitative data analysis, interpretation and integration.

Rules & Requirements

Prerequisites: BIO ENG 11, BIO ENG 114 or BIO ENG 202, or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 4 hours of laboratory and 2 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Conboy

Rules & Requirements

Prerequisites: MEC ENG 108, BIO ENG 102, MAT SCI 113 or equivalent

Credit Restrictions: Students will receive no credit for Mechanical Engineering C117 after completing Mechanical Engineering C215/Bioengineering C222.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Pruitt

Also listed as: MEC ENG C117

Objectives & Outcomes

Course Objectives: The course is separated into four parts spanning the principles of synthetic materials and surfaces, principles of biological materials, biological performance of materials and devices, and state-of-the-art materials design. Students are required to attend class and master the material therein. In addition, readings from the clinical, life and materials science literature are assigned. Students are encouraged to seek out additional reference material to complement the readings assigned. A mid-term examination is given on basic principles (parts 1 and 2 of the outline). A comprehensive final examination is given as well.
The purpose of this course is to introduce students to problems associated with the selection and function of biomaterials. Through class lectures and readings in both the physical and life science literature, students will gain broad knowledge of the criteria used to select biomaterials, especially in devices where the material-tissue or material-solution interface dominates performance. Materials used in devices for medicine, dentistry, tissue engineering, drug delivery, and the biotechnology industry will be addressed.

This course also has a significant design component (~35%). Students will form small teams (five or less) and undertake a semester-long design project related to the subject matter of the course. The project includes the preparation of a paper and a 20 minute oral presentation critically analyzing a current material-tissue or material-solution problem. Students will be expected to design improvements to materials and devices to overcome the problems identified in class with existing materials.

Student Learning Outcomes:
Apply math, science & engineering principles to the understanding of soft materials, surface chemistry, DLVO theory, protein adsorption kinetics, viscoelasticity, mass diffusion, and molecular (i.e., drug) delivery kinetics.

•
Design experiments and analyze data from the literature in the context of the class design project.
Apply core concepts in materials science to solve engineering problems related to the selection biomaterials, especially in devices where the material-tissue or material-solution interface dominates performance.
Develop an understanding of the social, safety and medical consequences of biomaterial use and regulatory issues associated with the selection of biomaterials in the context of the silicone breast implant controversy and subsequent biomaterials crisis.
Work independently and function on a team, and develop solid communication skills (oral, graphic & written) through the class design project.
•
Understanding of the origin of surface forces and interfacial free energy, and how they contribute to the development of the biomaterial interface and ultimately biomaterial performance.

Rules & Requirements

Prerequisites: MAT SCI 45 and BIO ENG 103 are required. BIO ENG 102 and BIO ENG 104 are strongly recommended

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Healy

Also listed as: MAT SCI C118

Rules & Requirements

Prerequisites: MEC ENG C85 / CIV ENG C30 or BIO ENG 102 (concurrent enrollment OK). Proficiency in MatLab or equivalent. Prior knowledge of biology or anatomy is not assumed

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Keaveny

Also listed as: MEC ENG C176

Rules & Requirements

Prerequisites: CHEM 3A; PHYSICS 7A and PHYSICS 7B; and BIO ENG 104 or equivalent transport course

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructors: Lee, Streets

Objectives & Outcomes

Course Objectives: Students will become familiar with research associated with BioMEMS and Lab-on-a-Chip technologies. Students will gain experience in using creative design to solve a technological problem. Students will learn basic microfabrication techniques. Working in engineering teams, students will learn how to properly characterize a novel device
by choosing and collecting informative metrics. Students will design and carry out carefully controlled experiments that will result in the analysis of quantitative data.

Student Learning Outcomes: Students will learn how to critically read BioMEMS and Lab-on-a-Chip primary literature. Students will learn how to use AutoCAD software to design microscale device features. Students will gain hands-on experience in basic photolithography and soft lithography. Students will get experience with a variety of fluid loading interfaces and
microscopy techniques. Students will learn how to design properly controlled uantitative experiments. Students will gain experience in presenting data to their peers in the form of powerpoint presentations and also at a poster symposium.

Rules & Requirements

Prerequisites: BIO ENG 104; and BIO ENG 121 (can be taken concurrently)

Credit Restrictions: Students will receive no credit for 121L after taking 221L.

Hours & Format

Fall and/or spring: 15 weeks - 6 hours of laboratory and 2 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Liepmann

Objectives & Outcomes

Course Objectives: The goal of this course is to give students the ability to understand problems in drug delivery. Emphasis is placed on the design and synthesis of new molecules for drug delivery.

Student Learning Outcomes: At the completion of this course students should be able to design new molecules to solve drug delivery problems.

Rules & Requirements

Prerequisites: BIO ENG 11 or CHEM 3B; BIO ENG 103 and BIO ENG 104

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Murthy

Rules & Requirements

Prerequisites: EL ENG 120 or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Bajcsy

Formerly known as: Electrical Engineering C125/Bioengineering C125

Also listed as: EL ENG C106A

Rules & Requirements

Prerequisites: EECS C106A / BIO ENG C125 or consent of the instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructors: Bajcsy, Sastry

Also listed as: EL ENG C106B

Objectives & Outcomes

Course Objectives: To introduce the biological databases and file formats commonly used in computational biology. (2) To familiarize students with the use of Unix scripting languages in bioinformatics workflows. (3) To introduce common algorithms for sequence alignment,
RNA structure prediction, phylogeny and clustering, along with fundamentals of probability, information theory and algorithmic complexity analysis.

Student Learning Outcomes: Students will be able to use knowledge from the lectures and lab sessions to write simple programs to parse bioinformatics file formats and execute basic algorithms, to analyze
algorithmic complexity, to navigate and (for simple cases) set up biological databases containing biological data (including sequences, genome annotations and protein structures), and to use basic statistics to interpret results of compbio analyses.

Rules & Requirements

Prerequisites: BIO ENG 11 or BIOLOGY 1A (may be taken concurrently); plus a programming course (ENGIN 7 or COMPSCI 61A)

Credit Restrictions: Students will receive no credit for BIO ENG 131 after completing BIO ENG 231. A deficient grade in BIO ENG 131 may be removed by taking BIO ENG C131.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1.5 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Holmes

Rules & Requirements

Prerequisites: BioE 11 or Bio 1A (may be taken concurrently), plus a programming course (ENGIN 7 or CS 61A)

Credit Restrictions: Students will receive no credit for BIO ENG C131 after completing BIO ENG 131, BIO ENG C131, or BIO ENG C131. A deficient grade in BIO ENG C131 may be removed by taking BIO ENG C131, or BIO ENG C131.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Holmes

Also listed as: CMPBIO C131

Objectives & Outcomes

Course Objectives: (1) To develop the skill of translating experimental design into computer code, (2) Develop familiarity with state-of-the-art infrastructure for wetlab automation, (3) Develop proficiency in software development

Student Learning Outcomes: students will be able to (1) Describe molecular biology entities and operations in terms of data structures, (2) Develop moderately-sized computer programs, (3) Write tests and benchmarking suites for biological algorithms (4) Explore different algorithmic approaches to problems and assess their relative merits and efficiencies, (5) Develop proficiency in conceiving and implementing software projects of their own design as they relate to biological problems

Rules & Requirements

Prerequisites: COMPSCI 61B, BIO ENG 11 and BIO ENG 103

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: J. Christopher Anderson

Rules & Requirements

Prerequisites: Upper division standing with background in differential equations and probability. Coursework in molecular and cell biology or biochemistry recommended

Credit Restrictions: Students will receive no credit for 135 after taking 235.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructors: Arkin, Bischofs-Pfeifer, Wolf

Rules & Requirements

Prerequisites: INTEGBI 135 or consent of instructor. For Electrical Engineering and Computer Sciences students: EL ENG 105, EL ENG 120 or COMPSCI 184

Credit Restrictions: Students will receive no credit for C135L after taking 135L.

Hours & Format

Fall and/or spring: 15 weeks - 6 hours of laboratory, 1 hour of discussion, and 1 hour of fieldwork per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Formerly known as: Integrative Biology 135L

Also listed as: EL ENG C145O/INTEGBI C135L

Objectives & Outcomes

Course Objectives: The purpose of this course is twofold:
•
to learn the fundamental concepts of designing devices to interact with the human body;
•
to enhance skills in mechanical engineering and bioengineering by analyzing the behavior of various complex biomedical problems;
•
To explore the transition of a device or discovery as it goes from “benchtop to bedside”.

Student Learning Outcomes: RELATIONSHIP OF THE COURSE TO ABET PROGRAM OUTCOMES
(a) an ability to apply knowledge of mathematics, science, and engineering
(b) an ability to design and conduct experiments, as well as to analyze and interpret data
(d) an ability to function on multi-disciplinary teams
(e) an ability to identify, formulate, and solve engineering problems
(f) an understanding of professional and ethical responsibility
(g) an ability to communicate effectively
(h) the broad education necessary to understand the impact of engineering solutions in a global, economic, environmental, and societal context
(i) a recognition of the need for, and an ability to engage in life-long learning
(j) a knowledge of contemporary issues
(k) an ability to use the techniques, skills, and modern engineering tools necessary for engineering practice.

Working knowledge of design considerations for creating a device to protect or aid the human body, force transfer and distribution, data analysis, and FDA approval process for new devices. Understanding of basic concepts in orthopaedic biomechanics and the ability to apply the appropriate engineering concepts to solve realistic biomechanical problems, knowing clearly the assumptions involved. Critical analysis of current literature and technology.

Rules & Requirements

Prerequisites: PHYSICS 7A, MATH 1A, and MATH 1B. Proficiency in MatLab or equivalent. Prior knowledge of biology or anatomy is not assumed

Credit Restrictions: There will be no credit given for MEC ENG C178 / BIO ENG C137 after taking MEC ENG 178.

Hours & Format

Fall and/or spring: 15 weeks - 1-3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: O'Connell

Formerly known as: Mechanical Engineering 178

Also listed as: MEC ENG C178

Objectives & Outcomes

Course Objectives: Designing and interpreting biological experiments
Learning how to plan, coordinate, and implement a genetic engineering project in a group format
To master the wetlab techniques of synthetic biology

Student Learning Outcomes: Students will be able to examine analytical data, interpret controls, and make decisions about next steps.
Students will be able to perform synthetic biology experiments including reagent preparation, DNA manipulation, analytical methods, and microbiological techniques.
Students will be able to understand responsible conduct expectations for wetlab experimentalists.
Students will be able to understand the techniques and protocols used in synthetic biology.
Students will be able to work within a team and develop communication skills.

Rules & Requirements

Prerequisites: BIO ENG 11 or BIOLOGY 1A

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture and 6 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Anderson

Objectives & Outcomes

Course Objectives: To build on optimization and statistical modeling to the field of machine learning techniques
To introduce the basics of optimization and statistical modeling techniques relevant to chemistry students
To utilize these concepts on problems relevant to the chemical sciences.

Student Learning Outcomes: Students will be able to understand the landscape and connections between numerical optimization, stand-alone statistical models, and machine learning techniques, and its relevance for chemical problems

Rules & Requirements

Prerequisites: MATH 53 and MATH 54; CHEM 120A or CHEM 120B or BIO ENG 103

Credit Restrictions: Students will receive no credit for BIO ENG C142 after completing BIO ENG 142. A deficient grade in BIO ENG C142 may be removed by taking BIO ENG 142.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternate method of final assessment during regularly scheduled final exam group (e.g., presentation, final project, etc.).

Instructor: Teresa Head-Gordon

Formerly known as: Bioengineering C142/Chemistry C142

Also listed as: CHEM C142

Rules & Requirements

Prerequisites: MATH 53 and MATH 54. Programming experience preferred but not required

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 2 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Head-Gordon

Objectives & Outcomes

Course Objectives: This course is designed to provide a theoretical framework for protein sequence and structure analysis using bioinformatics software tools. Students completing this course will be prepared for subsequent in-depth studies in bioinformatics, for algorithm development, and for the use of bioinformatics methods for biological discovery. It is aimed at two populations: students in the life sciences who need to become expert users of bioinformatics tools, and students in engineering and mathematics/computer science who wish to become the developers of the next generation of bioinformatics methods. As virtually all the problems in this field are very complex, there are many opportunities for research and development of new methods.

Student Learning Outcomes: Students completing this course are likely to find several potential areas of research of interest, which they may want to work on as independent study projects during undergraduate work, or take on as Master’s or Ph.D. thesis topics for advanced work.

Rules & Requirements

Prerequisites: Prior coursework in algorithms. No prior coursework in biology is required. This course includes no programming projects and prior experience in programming is not required

Credit Restrictions: BioE 244 or BioE C244L/PMB C244

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Sjolander

Formerly known as: Bioengineering C144/Plant and Microbial Biology C144

Rules & Requirements

Prerequisites: One upper-division course in molecular biology or biochemistry (e.g., MCELLBI C100A / CHEM C130 or equivalent); and Python programming (e.g. COMPSCI 61A) and experience using command-line tools in a Unix environment

Credit Restrictions: Bio Eng 244L or Bio Eng C244L/PMB C244L

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of laboratory and 2 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Sjolander

Formerly known as: Bioengineering C144L/Plant and Microbial Biology C144L

Objectives & Outcomes

Course Objectives: This course aims to equip students with a foundational understanding of computational and machine learning techniques used in genomics and computational biology.

Student Learning Outcomes: Students completing this course should have a better understanding of some of the challenges in machine learning as applied to biology
Students completing this course should have stronger programming skills.
Students completing this course should have the ability to apply simple statistical and machine learning techniques to complex genomics data

Rules & Requirements

Prerequisites: Bio 1A or BioE 11, Math 54, CS61B; CS70 or Math 55 recommended

Credit Restrictions: Students will receive no credit for BIO ENG 145 after completing BIO ENG 245. A deficient grade in BIO ENG 145 may be removed by taking BIO ENG 245.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Lareau

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Derenzo

Also listed as: EL ENG C145L

Rules & Requirements

Prerequisites: EE 16A & 16B

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Derenzo

Also listed as: EL ENG C145M

Objectives & Outcomes

Course Objectives: Students will become empowered to use basic coding approaches to access, work with, and
analyze biological data
Students will learn how to appropriately apply statistical tests to biological data
Students will learn how to select and evaluate methods and tools for data analysis
Students will understand how to grapple with the ethical considerations of biological data

Rules & Requirements

Prerequisites: Biology 1A; Biology 1B (can be taken concurrently); Data C8 or equivalent statistics and programming experience

Hours & Format

Fall and/or spring: 15 weeks - 4 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternate method of final assessment during regularly scheduled final exam group (e.g., presentation, final project, etc.).

Instructors: Brenner, Eisen

Also listed as: MCELLBI C146/PLANTBI C146

Objectives & Outcomes

Course Objectives: (1) To introduce the basics of Synthetic Biology, including quantitative cellular network characterization and modeling, (2) to introduce the principles of discovery and genetic factoring of useful cellular activities into reusable functions for design, (3) to inculcate the principles of biomolecular system design and diagnosis of designed systems, and (4) to illustrate cutting-edge applications in Synthetic Biology and to enhance skull sin analyzing and designing synthetic biological applications.

Student Learning Outcomes: The goals of this course are to enable students to: (1) design simple cellular circuitry to meet engineering specification using both rational/model-based and library-based approaches, (2) design experiments to characterize and diagnose operation of natural and synthetic biomolecular network functions, and (3) understand scientific, safety and ethical issues of synthetic biology.

Rules & Requirements

Prerequisites: MATH 53 and MATH 54; and BIO ENG 103 or consent of instructor

Credit Restrictions: Students will receive no credit for 147 after taking 247.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Arkin

Objectives & Outcomes

Course Objectives: (1) Learn the common engineered metabolic pathways for biofuel biosynthesis
(2) analytical methods
(3) synthetic biology approaches
(4) Industry technologies and opportunities

Student Learning Outcomes: Students will learn (1) the common pathways used for biofuel synthesis and framework for the biosynthesis of specialty chemicals, (2) analytical methods for quantitative measurements of metabolic pathways, (3) synthetic biology approaches for increasing overall pathway performance, and how to (4) utilize available online resources for culling information from large data sources.

Rules & Requirements

Prerequisites: CHEM 3A and BIO ENG 103

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Dueber

Objectives & Outcomes

Course Objectives: This course aims to equip students with practical proficiency in bioinformatics analysis of genomic data, as well as understanding of the biological, statistical, and computational underpinnings of this field.

Student Learning Outcomes: Students completing this course should have stronger programming skills, practical proficiency with essential bioinformatics methods that are applicable to genomics research, understanding of the statistics underlying these methods, and awareness of key aspects of genome function and challenges in the field of genomics.

Rules & Requirements

Prerequisites: MATH 54 or EECS 16A/B; COMPSCI 61A or equivalent Python course; BIOENG 11 or BIOLOGY 1A; and BIOENG 131. Introductory statistics or data science is recommended

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Lareau

Also listed as: CMPBIO C149

Objectives & Outcomes

Course Objectives: I.
Basic building blocks and governing forces: This part is intended to enhance the understanding of the structures and properties of biological basic building blocks and their governing forces to assemble the biological materials. This part covers the chemical structures of amino acids, ribonucleic acids, hydrocarbonates, and lipids, and their physical properties depending on the chemical and physical structures. In addition, governing forces (hydrogen bonding, ionic interaction, van der Waals interaction, hydrophobic interactions, etc) to assemble the basic building blocks to form nanostructures will be covered. Tools and methodologies to analyze the chemical structure of the molecules will be introduced. Quantitative analysis of the properties of biological basic building blocks will also be addressed.
II.
Case study of the molecular level structures of biological materials. This part is intended to study the examples of biological molecules to enhance understanding the assembly principle of biological materials, including collagens, keratins, spider webs, silks, bio-adhesives as protein based robust materials, bones, sea shells, diatoms, sponges, and, other biominerals as hierarchical nanostructures, and butterfly wings and insect eyes, other periodic structures for optical applications. Through the case study, we will learn how natural materials are designed to solve the challenging problem to be faced in the natural environments and exploit their design principle to develop novel functional materials and devices.
III.
Case study of the artificial nanomaterials and devices inspired by biological nature. This part is intended to enhance understanding the recently developed nanostructures and devices to mimic the natural biological materials and organisms. Hybrid functional nanomaterials and devices, such as biological basic building blocks conjugated with inorganic nanocomponents, such as quantum dots, nanowires, nanotubes will be discussed to fabricate various devices including, bio-sensor, bio-nano electronic materials and devices, bio-computing. Nano medicine and bio imaging will also be covered.
The goal is for the bioengineering students to gain sufficient chemical and physical aspects of biological materials through the case study of spider webs, silks, sea shells, diatoms, bones, and teeth, as well as recently developed self-assembled nanostructures inspired by nature.

Student Learning Outcomes: This course is intended for the undergraduate students interested in acquiring a background of recent development of bio-nanomaterials and bio-nanotechnology focused on the materials point of view. Through this course, students will understand the assembly principle of biological materials and their application in bio-nanotechnology.

Rules & Requirements

Prerequisites: BIO ENG 11 or BIOLOGY 1A; and CHEM 1A

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: S. W. Lee

Objectives & Outcomes

Course Objectives: We will study mass and momentum transport phenomena of microscale and nanoscale flow devices. Throughout the course, we will place an emphasis on bioanalytical microfluidic system applications where electrophoresis, electroosmosis, molecular diffusion, and/or Brownian motion effects dominate. Successful completion of the course will prepare students to design micro/nanofluidic engineering solutions, as well as critically assess academic and industrial developments in these areas.
The course is an introduction to the physicochemical dynamics associated with fluid flow in nanoscale and microscale devices for graduate students and advance undergraduate students. The course has been created in response to the active field of microfluidics and nanofluidics, as well as the associated interest from industry, government, and academic research groups. The course provides an theoretical treatment of micro/nanofluidic phenomena that complements the well-established laboratory and research content offered in the Department.

Student Learning Outcomes: 1.
To introduce students to the governing principles of fluid flow in microfluidic and nanofluidic regimes, with emphasis on phenomena relevant to bioanalytical devices.
2.
To provide students with an understanding of scaling laws that define the performance of microfluidic and nanofluidic systems.
3.
To provide students with a detailed investigation of applications that do and do not benefit from miniaturization.
4.
To give students adequate didactic background for critical assessment of literature reports and conference presentations regarding advances in the topical areas of microfluidics and nanofluidics.

Rules & Requirements

Prerequisites: BIO ENG 11 or CHEM 3B; BIO ENG 104, MEC ENG 106, or consent of instructor

Credit Restrictions: Students will receive no credit for 151 after taking 251.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Herr

Objectives & Outcomes

Course Objectives: To educate students on biopharmaceutical company entrepreneurship and innovation through team-based hands on virtual company creation
To educate students on careers in the biopharmaceutical industry
To educate students on the history of the field and industry, including key methodologies, technologies, scientists, entrepreneurs, and companies
To foster understanding and appreciation for the medical and societal impact of the biopharmaceutical field and industry
To introduce the key steps in the process of discovery, development and commercialization of novel therapeutics

Student Learning Outcomes: Entrepreneurship principles, including those defined by the Lean Launchpad approach (including the Business Model Canvas, the Minimum Viable Product and Customer Discovery).
The history of the biotech industry
The impact of the biopharmaceutical industry on medicine and society
The methods, product technologies and development methodologies that have driven the evolution of the field
The nature of the ecosystem and specific careers in the biopharmaceutical industry
The product design and development process (with a focus on biotherapeutics), including opportunities and challenges

Rules & Requirements

Prerequisites: Consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Kirn

Objectives & Outcomes

Course Objectives: To identify an existing or unmet clinical need and identify a nanomedicine that can provide a solution
To learn about chemical approaches used in nanomaterial synthesis and surface modification.
To learn how to read and critique the academic literature.
To understand the interaction of nanomaterials with proteins, cells, and biological systems.

Rules & Requirements

Prerequisites: MAT SCI 45 or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Messersmith

Also listed as: MAT SCI C157

Rules & Requirements

Prerequisites: CHEM 3A and PHYSICS 7B; and BIO ENG 102 or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Instructor: Marriott

Rules & Requirements

Prerequisites: BIO ENG 163 (may be taken concurrently)

Credit Restrictions: Students will receive no credit for Bioengineering 163L after taking Bioengineering 263L.

Hours & Format

Fall and/or spring: 15 weeks - 6 hours of laboratory and 2 hours of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Marriott

Rules & Requirements

Prerequisites: PHYSICS 7A and PHYSICS 7B; or PHYSICS 8A and PHYSICS 8B

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Fletcher

Rules & Requirements

Prerequisites: Prerequisites are introductory level skills in Python/Matlab; and either EECS 16A, EECS 16B, and EL ENG 120; or MATH 54, BIO ENG 105, and BIO ENG 101

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Conolly

Also listed as: EL ENG C145B

Objectives & Outcomes

Course Objectives: Discuss limitations to each targeted approach including non-specific binding, unbound probe clearance, signal decay, etc.
Discuss the design of targeted molecular contrast agents for each modality across myriad biological applications
Establish a foundational understanding of MRI (multi-spectral), PET/SPECT, Ultrasound (including photo-acoustic imaging), and emerging methods including MPI
Establish proficiency in the use of MATLAB as a tool for analyzing biomedical imaging data
Reinforce mathematical principles relevant to image analysis including linear algebra, convolution and differential equations
To discuss imaging ethics in the context of data interpretation
To expose students interested in biomedical research or clinical practice to fundamentals of modern imaging methods and interpretation
To learn quantitative approaches to analyze biomedical images (includes pharmacokinetic models, attenuation correction, cross modality registration, etc.)

Student Learning Outcomes: Analyze imaging data derived from imaging studies using commonly utilized image processing techniques
Critically evaluate scientific publications in the molecular imaging space.

Understand the devices, techniques and protocols used for in vivo imaging in research and clinical settings

Rules & Requirements

Prerequisites: BIO ENG C165 or BIO ENG 163; and BIO ENG 101 plus BIO ENG 105 or EECS 16A plus EECS 16B

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Vandsburger

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Fletcher

Objectives & Outcomes

Course Objectives: Understand the close interface between studies of the nervous system and technology

Student Learning Outcomes: The course will review the utilization, development and implementation of a wide diversity of neural engineering technologies to the study of the brain. Students will discuss the bidirectional road between the two approaches.
The overreaching goal of this course is to expose student interested in neural engineering to the remarkable history of neuroethological approaches that have been a foundation of discoveries in the field.

Rules & Requirements

Prerequisites: BIO ENG 105; and BIO ENG 101 or EECS 16A and EECS 16B; or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructor: Yartsev

Rules & Requirements

Prerequisites: Chemistry 1B or Chemistry 4B, Mathematics 1B, Biology 1A

Repeat rules: Course may be repeated for credit under special circumstances: Repeatable when topic changes with consent of instructor.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Instructors: Bell, Blanch, Clark, Smit, C. Somerville

Also listed as: CHEM C138/CHM ENG C195A/PLANTBI C124

Rules & Requirements

Prerequisites: Consent of instructor

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1-4 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam required.

Rules & Requirements

Prerequisites: Senior standing

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture and 2 hours of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam not required.

Instructor: Herr

Rules & Requirements

Prerequisites: Upper division technical GPA 3.3 or higher and consent of instructor and adviser

Repeat rules: Course may be repeated for credit up to a total of 8 units.

Hours & Format

Fall and/or spring: 15 weeks - 3-4 hours of independent study per week

Summer:
8 weeks - 1.5-7.5 hours of independent study per week
10 weeks - 1.5-9 hours of independent study per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Final exam not required.

Objectives & Outcomes

Course Objectives: •
To introduce students to bioengineering research as it is performed at Berkeley and at other institutions
•
To give students opportunities to connect their own work to work in the field overall
•
To give students an opportunity to meet with speakers who can inform and contribute to their post-graduation career paths

Student Learning Outcomes: To introduce students to the breadth of bioengineering research, both here at Berkeley and at other institutions, and help them to connect their work here at Berkeley to the field overall.

Rules & Requirements

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1 hour of seminar per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

Instructor: Faculty

Rules & Requirements

Prerequisites: Junior or senior status, consent of instructor and faculty adviser

Repeat rules: Course may be repeated for credit up to a total of 8 units.

Hours & Format

Fall and/or spring: 15 weeks - 2-4 hours of independent study per week

Summer: 10 weeks - 3-9 hours of independent study per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Letter grade. Alternative to final exam.

Rules & Requirements

Prerequisites: Upper division standing and good academic standing. (2.0 grade point average and above)

Credit Restrictions: Enrollment is restricted; see the Introduction to Courses and Curricula section of this catalog.

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1-4 hours of directed group study per week

Summer:
6 weeks - 2.5-10 hours of directed group study per week
8 weeks - 1.5-7.5 hours of directed group study per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

Rules & Requirements

Credit Restrictions: Enrollment is restricted; see the Introduction to Courses and Curricul a section of this catalog.

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 0 hours of independent study per week

Summer:
6 weeks - 2.5-10 hours of independent study per week
8 weeks - 1.5-7.5 hours of independent study per week
10 weeks - 1.5-6 hours of independent study per week

Additional Details

Subject/Course Level: Bioengineering/Undergraduate

Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

Rules & Requirements

Prerequisites: Enrollment in PhD Program in Bioengineering or consent of instructor

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1 hour of seminar per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Offered for satisfactory/unsatisfactory grade only.

Objectives & Outcomes

Course Objectives: The content of the class is designed considering the NSF Standards of Ethical Conduct and the NIH Ethical Guidelines & Regulations in mind, and to serve as the Responsible Conduct of Research training for our PhD program.

Student Learning Outcomes: To prepare bioengineering PhD students to perform their research and design responsibly.

Rules & Requirements

Prerequisites: Open only to Bioengineering graduate students

Hours & Format

Fall and/or spring: 10 weeks - 1 hour of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Offered for satisfactory/unsatisfactory grade only.

Instructor: Terry Johnson

Objectives & Outcomes

Course Objectives: The goal of this course to establish fundamental understanding of cell engineering technologies and of the key biological paradigms, upon which cell engineering is based, with the focus on biomedical applications of cell engineering.

Student Learning Outcomes: At the completion of this course students will understand how bioengineering technologies address the deliberate control of cell properties (and how this advances biomedicine); and students will learn the main concepts and current views on key attributes of animal cells (somatic, embryonic, pluripotent, germ-line; with the focus on mammalian cells).

Rules & Requirements

Prerequisites: BIOLOGY 1A or BIO ENG 11; or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 2 hours of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Conboy

Objectives & Outcomes

Course Objectives: The goal of this course to provide students with conceptual and practical understanding of cell and tissue bioengineering.

Student Learning Outcomes: At the completion of this course, students will learn key cellular bioengineering laboratory techniques, will develop a conceptual and theoretical understanding of the reliability and limitations of these techniques and will enhance their skills in quantitative data analysis, interpretation and integration.

Rules & Requirements

Prerequisites: BIO ENG 114 or BIO ENG 202, or BIO ENG 11; or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 9 hours of laboratory and 1 hour of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Conboy

Objectives & Outcomes

Course Objectives: The course is separated into four parts spanning the principles of synthetic materials and surfaces, principles of biological materials, biological performance of materials and devices, and state-of-the-art materials design. Students are required to attend class and master the material therein. In addition, readings from the clinical, life and materials science literature are assigned. Students are encouraged to seek out additional reference material to complement the readings assigned. A mid-term examination is given on basic principles (parts 1 and 2 of the outline). A comprehensive final examination is given as well.
The purpose of this course is to introduce students to problems associated with the selection and function of biomaterials. Through class lectures and readings in both the physical and life science literature, students will gain broad knowledge of the criteria used to select biomaterials, especially in devices where the material-tissue or material-solution interface dominates performance. Materials used in devices for medicine, dentistry, tissue engineering, drug delivery, and the biotechnology industry will be addressed.

This course also has a significant design component (~35%). Students will form small teams (five or less) and undertake a semester-long design project related to the subject matter of the course. The project includes the preparation of a paper and a 20 minute oral presentation critically analyzing a current material-tissue or material-solution problem. Students will be expected to design improvements to materials and devices to overcome the problems identified in class with existing materials.

Student Learning Outcomes: Work independently and function on a team, and develop solid communication skills (oral, graphic & written) through the class design project.
•
Develop an understanding of the social, safety and medical consequences of biomaterial use and regulatory issues associated with the selection of biomaterials in the context of the silicone breast implant controversy and subsequent biomaterials crisis.
•
Design experiments and analyze data from the literature in the context of the class design project.

•
Understanding of the origin of surface forces and interfacial free energy, and how they contribute to the development of the biomaterial interface and ultimately biomaterial performance.
•
Apply math, science & engineering principles to the understanding of soft materials, surface chemistry, DLVO theory, protein adsorption kinetics, viscoelasticity, mass diffusion, and molecular (i.e., drug) delivery kinetics.
•
Apply core concepts in materials science to solve engineering problems related to the selection biomaterials, especially in devices where the material-tissue or material-solution interface dominates performance.

Rules & Requirements

Prerequisites: MAT SCI 45; and CHEM C130 / MCELLBI C100A or ENGIN 40; and BIO ENG 102 and 104 recommended

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Healy

Also listed as: MAT SCI C208

Objectives & Outcomes

Course Objectives: The purpose of this course is twofold:
•
to learn the fundamental concepts of orthopaedic biomechanics;
•
to enhance skills in mechanical engineering and bioengineering by analyzing the mechanical behavior of various complex biomedical problems.

Student Learning Outcomes: Working knowledge of various engineering concepts such as composite beam theory, beam-on-elastic-foundation theory, Hertz contact theory and MATLAB-based optimization design analysis. Understanding of basic concepts in orthopaedic biomechanics and the ability to apply the appropriate engineering concepts to solve realistic biomechanical problems, knowing clearly the assumptions involved.

Rules & Requirements

Prerequisites: ME C85/CE C30 or Bio Eng 102; concurrent enrollment OK. Proficiency in MatLab or equivalent. Prior knowledge of biology or anatomy is not assumed

Credit Restrictions: Students will not receive credit for this course if they have taken ME C176/Bio E C119.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 1 hour of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructors: O'Connell, Keaveny

Also listed as: MEC ENG C210

Rules & Requirements

Prerequisites: Undergraduate cell biology or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Kumar

Rules & Requirements

Prerequisites: 106 and 109 (106 and 109 may be taken concurrently)

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Formerly known as: Mechanical Engineering 212

Also listed as: MEC ENG C212

Rules & Requirements

Prerequisites: 106 or equivalent; 265A or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructors: Berger, Liepmann

Also listed as: MEC ENG C213

Rules & Requirements

Prerequisites: 102A, 176, 185; graduate standing or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Also listed as: MEC ENG C214

Objectives & Outcomes

Course Objectives: This course, which is open to graduate students in diverse disciplines ranging from engineering to biology to chemistry and physics, is aimed at exposing students to subcellular biomechanical phenomena spanning scales from molecules to the whole cell.

Student Learning Outcomes: The students will develop tools and skills to (1) understand and analyze subcelluar biomechanics and transport phenomena, and (2) ultimately apply these skills to novel biological and biomedical applications.

Rules & Requirements

Prerequisites: MATH 54, PHYSICS 7A; BIO ENG 102 or MEC ENG C85; or instructor’s consent

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Mofrad

Also listed as: MEC ENG C216

Rules & Requirements

Prerequisites: BIO ENG 115. Open to seniors with consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Healy

Also listed as: MAT SCI C216

Rules & Requirements

Prerequisites: Graduate standing in engineering or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Dharan

Also listed as: INTEGBI C217/MEC ENG C217

Rules & Requirements

Prerequisites: Consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 6 hours of laboratory and 1 hour of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Conboy

Also listed as: MCELLBI C237

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Tullman-Ercek

Also listed as: CHM ENG C270

Rules & Requirements

Prerequisites: Cell and tissue engineering; upper division cell biology course or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture and 6 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Li

Rules & Requirements

Prerequisites: Chemistry 3A, Physics 7A and 7B, Electrical Engineering 143 or equivalent

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Summer:
6 weeks - 7.5 hours of lecture per week
8 weeks - 5.5 hours of lecture per week
10 weeks - 4.5 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: L. Lee

Objectives & Outcomes

Course Objectives: Students will become familiar with research associated with BioMEMS and Lab-on-a-Chip technologies. Students will gain experience in using creative design to solve a technological problem. Students will learn basic microfabrication techniques. Working in engineering teams, students will learn how to properly characterize a novel device
by choosing and collecting informative metrics. Students will design and carry out carefully controlled experiments that will result in the analysis of quantitative data.

Student Learning Outcomes: Students will learn how to critically read BioMEMS and Lab-on-a-Chip primary literature. Students will learn how to use AutoCAD software to design microscale device features. Students will gain hands-on experience in basic photolithography and soft lithography. Students will get experience with a variety of fluid loading interfaces and
microscopy techniques. Students will learn how to design properly controlled uantitative experiments. Students will gain experience in presenting data to their peers in the form of powerpoint presentations and also at a poster symposium.

Rules & Requirements

Prerequisites: BIO ENG 104, BIO ENG 221, and/or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 6 hours of laboratory and 2 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructors: Liepmann, Streets

Rules & Requirements

Credit Restrictions: Students should not receive credit if they've taken ME ME C117 or Bio Eng C117.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Also listed as: MEC ENG C215

Rules & Requirements

Prerequisites: MECENG 108, BIOENG 102, MATSCI 113 or equivalent

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Also listed as: MEC ENG C223

Objectives & Outcomes

Course Objectives: The goal of this course is to give students the ability to understand problems in drug delivery. Emphasis is placed on the design and synthesis of new molecules for drug delivery.

Student Learning Outcomes: At the completion of this course students should be able to design new molecules to solve drug delivery problems.

Rules & Requirements

Prerequisites: BIO ENG 11 or CHEM 3B; BIO ENG 103; and BIO ENG 104

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Murthy

Objectives & Outcomes

Course Objectives: (1) Introduce students to the atomic structure of macromolecules,
2) review methods for structure determination, (3) describe the basic theory of diffraction, and (4) provide students with a detailed knowledge of macromolecular crystallography. At the end of the course students will have a solid theoretical and practical understanding of how macromolecular structures are determined to atomic resolution using crystallographic methods. The application of the method to problems in biomolecular engineering will be reviewed.

Student Learning Outcomes: The students will be able to (1) interpret diffraction data to determine reciprocal and real space parameters, (2) plan diffraction experiments, (3) use computational methods to solve the crystallographic phase problem (an inverse problem), (4) interpret complex 3-dimensional maps to build atomic models, (5) determine which optimization methods are appropriate for obtaining a refined, validated model, and (6) apply the knowledge to the engineering of biomolecules.

Rules & Requirements

Prerequisites: Consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Paul Adams

Rules & Requirements

Prerequisites: Consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructors: Arkin, Keasling

Also listed as: CHM ENG C295L

Rules & Requirements

Prerequisites: BIO ENG 11 or BIOLOGY 1A (may be taken concurrently); and a programming course (ENGIN 7 or COMPSCI 61A)

Credit Restrictions: Students will receive no credit for BIO ENG 231 after completing BIO ENG 131, or BIO ENG C231. A deficient grade in BIO ENG 231 may be removed by taking BIO ENG C231, or BIO ENG C231.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1.5 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Holmes

Rules & Requirements

Prerequisites: BIO ENG 11 or BIOLOGY 1A (may be taken concurrently); and a programming course (ENGIN 7 or COMPSCI 61A)

Credit Restrictions: Students will receive no credit for BIO ENG C231 after completing BIO ENG 231. A deficient grade in BIO ENG C231 may be removed by taking BIO ENG 231, or BIO ENG 231.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Holmes

Also listed as: CMPBIO C231

Objectives & Outcomes

Course Objectives: (1) To introduce the basic biology and engineering principles for constructing genetic devices including biochemical devices, microbiological devices, genetic circuits, eukaryotic devices, and developmental devices, (2) To familiarize students with current literature examples of genetic devices and develop literature searching skills; (3) To develop the students' ability to apply computational tools to the design of genetic devices.

Student Learning Outcomes: Students will be able to (1) use mathematical models to describe the dynamics of genetic devices, (2) comprehend and evaluate publications related to any type of genetic device, (3) perform a thorough literature search, (4) evaluate the technical plausibility of a proposed genetic device, (5) analyze a design challenge and propose a plausible solution to it in the form of a genetic device, and (6) assess any ethical or safety issues associated with a proposed genetic device.

Rules & Requirements

Prerequisites: ENGIN 7 or COMPSCI 61A; MATH 54; CHEM 3A; and BIO ENG 103

Credit Restrictions: Students will receive no credit for 232 after taking 132.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Anderson

Rules & Requirements

Prerequisites: Designed for graduates with background in differential equations and probability. Course work in molecular cell biology or biochemistry helpful

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructors: Arkin, Bischofs-Pfeifer, Wolf

Objectives & Outcomes

Course Objectives: The purpose of this course is twofold:
•
to learn the fundamental concepts of designing devices that interact with the human body;
•
to enhance skills in mechanical engineering and bioengineering by analyzing the behavior of various complex biomedical problems;
•
To explore the transition of a device or discovery as it goes from “benchtop to bedside”.
•
Three separate written projects evaluating devices that interact with the body. Projects will focus on 1) biomechanical analysis, 2) FDA regulations and procedures, and 3) design lifecycle.

Student Learning Outcomes: Working knowledge of design considerations for creating a device to protect or aid the human body, force transfer and distribution, data analysis, and FDA approval process for new devices. Understanding of basic concepts in orthopaedic biomechanics and the ability to apply the appropriate engineering concepts to solve realistic biomechanical problems, knowing clearly the assumptions involved. Critical analysis of current literature and technology.

Rules & Requirements

Prerequisites: Proficiency in MatLab or equivalent. Prior knowledge of biology or anatomy is not assumed

Credit Restrictions: There will be no credit given for MEC ENG C178 / BIO ENG C137 after taking MEC ENG 178.

Hours & Format

Fall and/or spring: 15 weeks - 1-3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: O'Connell

Also listed as: MEC ENG C278

Objectives & Outcomes

Course Objectives: To introduce the most commonly used statistical models and associated inference techniques for the analysis and organization of biological sequences, with a focus on models based on evolutionary theory.

Student Learning Outcomes: Students will be familiar with the bioinformatics literature and underyling theory for discrete Markov processes, Bayesian networks, stochastic grammars, birth-death processes, Chinese restaurant processes, data compression algorithms, and related methods such as dynamic programming and MCMC.

Rules & Requirements

Prerequisites: Recommended preparation: MATH 53 (multivariable calculus), MATH 54 (linear algebra), MATH 126 (partial differential equations); or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Holmes

Objectives & Outcomes

Course Objectives: To build on optimization and statistical modeling to the field of machine learning techniques
To introduce the basics of optimization and statistical modeling techniques relevant to chemistry students
To utilize these concepts on problems relevant to the chemical sciences.

Student Learning Outcomes: Students will be able to understand the landscape and connections between numerical optimization, stand-alone statistical models, and machine learning techniques, and its relevance for chemical problems.

Rules & Requirements

Prerequisites: Math 53 and Math 54; Chem 120A or 120B or BioE 103; or consent of intructor

Credit Restrictions: Students will receive no credit for BIO ENG C242 after completing BIO ENG 242. A deficient grade in BIO ENG C242 may be removed by taking BIO ENG 242.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Teresa Head-Gordon

Formerly known as: Bioengineering C242/Chemistry C242

Also listed as: CHEM C242

Rules & Requirements

Prerequisites: MATH 53 and MATH 54; and programming experience preferred but not required

Credit Restrictions: Students will receive no credit for 243 after taking 143.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 2 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Head-Gordon

Objectives & Outcomes

Course Objectives: This course is designed to provide a theoretical framework for protein sequence and structure analysis using bioinformatics software tools. Students completing this course will be prepared for subsequent in-depth studies in bioinformatics, for algorithm development, and for the use of bioinformatics methods for biological discovery. It is aimed at two populations: students in the life sciences who need to become expert users of bioinformatics tools, and students in engineering and mathematics/computer science who wish to become the developers of the next generation of bioinformatics methods. As virtually all the problems in this field are very complex, there are many opportunities for research and development of new methods.

Student Learning Outcomes: Students completing this course are likely to find several potential areas of research of interest, which they may want to work on as independent study projects during undergraduate work, or take on as Master’s or Ph.D. thesis topics for advanced work.

Rules & Requirements

Prerequisites: Prior coursework in algorithms (e.g., COMPSCI 170) is highly recommended. The class does not include programming, and no prior programming experience is required, although students need to be comfortable reading and writing pseudocode (precise text descriptions of algorithms

Credit Restrictions: BioE 144 or previous BioE/PMB C144

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Sjolander

Formerly known as: Bioengineering C244/Plant and Microbial Biology C244

Rules & Requirements

Prerequisites: One upper-division course in molecular biology or biochemistry (e.g., MCELLBI C100A/CHEM C130). Python programming (e.g., COMPSCI 61A) and experience using command-line tools in a Unix environment

Credit Restrictions: BioE 144L or BioE C144L/PMB C144L

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of laboratory and 2 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Sjolander

Formerly known as: Bioengineering C244L/Plant and Microbial Biology C244L

Objectives & Outcomes

Course Objectives: This course aims to equip students with a foundational understanding of computational and machine learning techniques used in genomics and computational biology.

Student Learning Outcomes: Students completing this course should have a better understanding of some of the challenges in machine learning as applied to biology
Students completing this course should have stronger programming skills.
Students completing this course should have the ability to apply simple statistical and machine learning techniques to complex genomics data

Rules & Requirements

Prerequisites: Bio 1A or BioE 11, Math 54, CS61B; CS70 or Math 55 recommended

Credit Restrictions: Students will receive no credit for BIO ENG 245 after completing BIO ENG 145.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Lareau

Objectives & Outcomes

Course Objectives: (1) To introduce the basics of Synthetic Biology, including quantitative cellular network characterization and modeling, (2) to introduce the principles of discovery and genetic factoring of useful cellular activities into reusable functions for design, (3) to inculcate the principles of biomolecular system design and diagnosis of designed systems, and (4) to illustrate cutting-edge applications in Synthetic Biology and to enhance skull sin analyzing and designing synthetic biological applications.

Student Learning Outcomes: The goals of this course are to enable students to: (1) design simple cellular circuitry to meet engineering specification using both rational/model-based and library-based approaches, (2) design experiments to characterize and diagnose operation of natural and synthetic biomolecular network functions, and (3) understand scientific, safety and ethical issues of synthetic biology.

Rules & Requirements

Prerequisites: MATH 53, MATH 54, and BIO ENG 103; or consent of instructor

Credit Restrictions: Students will receive no credit for 247 after taking 147.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Arkin

Rules & Requirements

Prerequisites: CHEM 3A; and MCELLBI C100A/CHEM C130A or equivalent

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Dueber

Objectives & Outcomes

Course Objectives: This course aims to equip students with practical proficiency in bioinformatics analysis of genomic data, as well as understanding of the biological, statistical, and computational underpinnings of this field.

Student Learning Outcomes: Students completing this course should have stronger programming skills, practical proficiency with essential bioinformatics methods that are applicable to genomics research, understanding of the statistics underlying these methods, and awareness of key aspects of genome function and challenges in the field of genomics.

Rules & Requirements

Prerequisites: Math 54 or EECS 16A/B; CS 61A or another course in python; BioE 11 or Bio 1a; and BioE 131. Introductory statistics or data science is recommended

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Lareau

Also listed as: CMPBIO C249

Objectives & Outcomes

Course Objectives: To review the current literature regarding the use of nanomaterials in medical applications; (2) To describe approaches to nanomaterial synthesis and surface modification; (3) To understand the interaction of nanomaterials with proteins, cells and biological systems; (4) To familiarize students with proposal writing and scientific peer review.

Student Learning Outcomes: Students should be able to (1) identify the important properties of metal, polymer and ceramic nanomaterials used in healthcare; (2) understand the role of size, shape and surface chemistry of nanomaterials in influencing biological fate and performance; (3) understand common methods employed for surface modification of nanomaterials; (4) comprehend the range of cell-nanomaterial interactions and methods for assaying these interactions; (5) read and critically review the scientific literature relating to nanomedicine; (6) formulate and design an experimental nanomedicine research project; (7) understand the principles of the peer review system.

Rules & Requirements

Prerequisites: Graduate Standing

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Messersmith

Also listed as: MAT SCI C250

Objectives & Outcomes

Course Objectives: The course is an introduction to the physicochemical dynamics associated with fluid flow in nanoscale and microscale devices for graduate students and advance undergraduate students. The course has been created in response to the active field of microfluidics and nanofluidics, as well as the associated interest from industry, government, and academic research groups. The course provides an theoretical treatment of micro/nanofluidic phenomena that complements the well-established laboratory and research content offered in the Department.
We will study mass and momentum transport phenomena of microscale and nanoscale flow devices. Throughout the course, we will place an emphasis on bioanalytical microfluidic system applications where electrophoresis, electroosmosis, molecular diffusion, and/or Brownian motion effects dominate. Successful completion of the course will prepare students to design micro/nanofluidic engineering solutions, as well as critically assess academic and industrial developments in these areas.

Student Learning Outcomes: 1.
To introduce students to the governing principles of fluid flow in microfluidic and nanofluidic regimes, with emphasis on phenomena relevant to bioanalytical devices.
2.
To provide students with an understanding of scaling laws that define the performance of microfluidic and nanofluidic systems.
3.
To provide students with a detailed investigation of applications that do and do not benefit from miniaturization.
4.
To give students adequate didactic background for critical assessment of literature reports and conference presentations regarding advances in the topical areas of microfluidics and nanofluidics.

Rules & Requirements

Prerequisites: BIO ENG 11 or CHEM 3B; and BIO ENG 104 or MEC ENG 106; or consent of instructor

Credit Restrictions: Students will receive no credit for 251 after taking 151.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Herr

Objectives & Outcomes

Course Objectives: (1) To expose students to clinical areas with major unmet need; (2) Expose students to current state of the art in therapy solutions for the above clinical need; (3) Stimulate innovation concept targeting high-impact clinical needs

Student Learning Outcomes: Students will be able to (1) Immerse in an enabling innovation environment stemming from the solution ideas by the students and mentor faculties; (2) Obtain potential avenues to enable capstone projects, UCSF collaborations, SBIR, etc.

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Hossiany

Objectives & Outcomes

Course Objectives: To educate students on careers in the biopharmaceutical industry
To educate students on the history of the field and industry, including key methodologies, technologies, scientists, entrepreneurs, and companies
To foster understanding and appreciation for the medical and societal impact of the biopharmaceutical field and industry
To introduce the key steps in the process of discovery, development and commercialization of novel therapeutics
o educate students on biopharmaceutical company entrepreneurship and innovation through team-based hands on virtual company creation

Student Learning Outcomes: Entrepreneurship principles, including those defined by the Lean Launchpad approach (including the Business Model Canvas, the Minimum Viable Product and Customer Discovery)
The history of the biotech industry
The impact of the biopharmaceutical industry on medicine and society
The methods, product technologies and development methodologies that have driven the evolution of the field
The nature of the ecosystem and specific careers in the biopharmaceutical industry
The product design and development process (with a focus on biotherapeutics), including opportunities and challenges

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Kirn

Objectives & Outcomes

Course Objectives: •
understand how 2D impulse response or 2D spatial frequency transfer function (or Modulation Transfer Function) allow one to quantify the spatial resolution of an imaging system.
•
understand 2D sampling requirements to avoid aliasing
•
understand 2D filtered backprojection reconstruction from projections based on the projection-slice theorem of Fourier Transforms
•
understand the concept of image reconstruction as solving a mathematical inverse problem.
•
understand the limitations of poorly conditioned inverse problems and noise amplification
•
understand how diffraction can limit resolution---but not for the imaging systems in this class
•
understand the hardware components of an X-ray imaging scanner
•
•
understand the physics and hardware limits to spatial resolution of an X-ray imaging system
•
understand tradeoffs between depth, contrast, and dose for X-ray sources
•
understand resolution limits for CT scanners
•
understand how to reconstruct a 2D CT image from projection data using the filtered backprojection algorithm
•
understand the hardware and physics of Nuclear Medicine scanners
•
understand how PET and SPECT images are created using filtered backprojection
•
understand resolution limits of nuclear medicine scanners
•
understand MRI hardware components, resolution limits and image reconstruction via a 2D FFT
•
understand how to construct a medical imaging scanner that will achieve a desired spatial resolution specification.

Student Learning Outcomes: •
students will be tested for their understanding of the key concepts above
•
undergraduate students will apply to graduate programs and be admitted
•
students will apply this knowledge to their research at Berkeley, UCSF, the national labs or elsewhere
•
students will be hired by companies that create, sell, operate or consult in biomedical imaging

Rules & Requirements

Prerequisites: Undergraduate level course work covering integral and differential calculus, two classes in engineering-level physics, introductory level linear algebra, introductory level statistics, at least 1 course in LTI system theory including (analog convolution, Fourier transforms, and Nyquist sampling theory). The recommended undergrad course prerequisites are introductory level skills in Python or Matlab and either EECS 16A, EECS 16B and EL ENG 120, or MATH 54, BIO ENG 101, and BIO ENG 105

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Conolly

Also listed as: EL ENG C261/NUC ENG C231

Rules & Requirements

Prerequisites: 102 or consent of instructor, and Chemistry 3A and Physics 7B

Credit Restrictions: Students will receive no credit for 263 after taking 163.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Marriott

Rules & Requirements

Prerequisites: BIO ENG 263; experience in a research lab; and consent of instructor

Credit Restrictions: Students will receive no credit for 263L after taking 163L.

Hours & Format

Fall and/or spring: 15 weeks - 6 hours of laboratory and 2 hours of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Marriott

Objectives & Outcomes

Course Objectives: Graduate level understanding of physics, hardware, and systems engineering description of image formation, and image reconstruction in MRI. Experience in Imaging with different MR Imaging systems. This course should enable students to begin graduate level research at Berkeley (Neuroscience labs, EECS and Bioengineering), LBNL or at UCSF (Radiology and Bioengineering) at an advanced level and make research-level contribution

Rules & Requirements

Prerequisites: EL ENG 120 or BIO ENG C165/EL ENG C145B or consent of instructor

Credit Restrictions: Students will receive no credit for Bioengineering C265/El Engineering C225E after taking El Engineering 265.

Repeat rules: Course may be repeated for credit under special circumstances: Students can only receive credit for 1 of the 2 versions of the class,BioEc265 or EE c225e, not both

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 3 hours of laboratory per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructors: Conolly, Vandsburger

Also listed as: EL ENG C225E/NUC ENG C235

Objectives & Outcomes

Course Objectives: Discuss limitations to each targeted approach including non-specific binding, unbound probe clearance, signal decay, etc
Discuss the design of targeted molecular contrast agents for each modality across myriad biological applications
Establish a foundational understanding of MRI (multi-spectral), PET/SPECT, Ultrasound (including photo-acoustic imaging), and emerging methods including MPI
Establish proficiency in the use of MATLAB as a tool for analyzing biomedical imaging data
Reinforce mathematical principles relevant to image analysis including linear algebra, convolution and differential equations
To discuss imaging ethics in the context of data interpretation
To expose students interested in biomedical research or clinical practice to fundamentals of modern imaging methods and interpretation
To learn quantitative approaches to analyze biomedical images (includes pharmacokinetic models, attenuation correction, cross modality registration, etc.)

Student Learning Outcomes: Analyze imaging data derived from imaging studies using commonly utilized image processing techniques
Critically evaluate scientific publications in the molecular imaging space.
Understand the devices, techniques and protocols used for in vivo imaging in research and clinical settings

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Vandsburger

Objectives & Outcomes

Course Objectives: Understand the close interface between studies of the nervous system and technology

Student Learning Outcomes: The course will review the utilization, development and implementation of a wide diversity of neural engineering technologies to the study of the brain. Students will discuss the bidirectional road between the two approaches
The overreaching goal of this course is to expose student interested in neural engineering to the remarkable history of neuroethological approaches that have been a foundation of discoveries in the field.

Rules & Requirements

Prerequisites: BIO ENG 105; and BIO ENG 101 or EECS 16A and EECS 16B; or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Yartsev

Objectives & Outcomes

Course Objectives: Objectives
● Communications skills and best practices
● Research ethics in translational medicine
● Professional development for MTM graduate students

Student Learning Outcomes: MTM students will become aware of ethical issues commonly confronted in
translational medicine and learn how to evaluate and act accordingly. They will also
leave capable of independently considering new ethical issues that arise during their
careers.

Rules & Requirements

Prerequisites: Open only to students in the Masters of Translational Medicine Graduate program

Hours & Format

Fall and/or spring: 15 weeks - 1 hour of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructors: Johnson, Terry

Rules & Requirements

Prerequisites: Major in physical science such as chemistry, physics, etc., or engineering; consent of advisor or instructor

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructors: Gronsky, S.W. Lee, Wu

Also listed as: MAT SCI C261/NSE C201/PHYSICS C201

Rules & Requirements

Prerequisites: Biology 1A; Chemistry 1B or 4B, Mathematics 1B

Repeat rules: Course may be repeated for credit under special circumstances: Repeatable when topic changes with consent of instructor.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructors: Bell, Blanch, Clark, Smit, C. Somerville

Also listed as: CHEM C238/CHM ENG C295A/PLANTBI C224

Objectives & Outcomes

Course Objectives: •
Develop skills in translating physical problem statement into quantitative applied math construction
•
Emphasis will be on constructing problems statements into mathematical equations and boundary conditions.

Student Learning Outcomes: •
Use quantitative applied math construction to estimate dominant parameters or dimensionless groups in cutting-edge, industry-relevant problem statements
•
Students become well-versed in quantitative analysis of real life products and therapeutic applications

Rules & Requirements

Prerequisites: Calculus (MATH 54); BIO ENG 104 (preferred but not required); and/or consent of instructor

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Syed Hossiany

Rules & Requirements

Prerequisites: Consent of instructor

Credit Restrictions: One hour of lecture per week per unit.

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1-4 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Hours & Format

Fall and/or spring: 15 weeks - 3 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Offered for satisfactory/unsatisfactory grade only.

Instructors: Keaveny, Pruitt

Also listed as: MEC ENG C290X

Hours & Format

Fall and/or spring: 15 weeks - 2 hours of lecture per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructor: Rodriguez

Objectives & Outcomes

Course Objectives: The objective of the one year professional MTM program is to develop engineering leaders who can synthesize the technical, environmental, economic, and social issues involved in the design and operation of complex engineering devices, systems, and organizations. Students will develop and demonstrate this skill at synthesis through the capstone project.

Student Learning Outcomes: Projects will provide practical instruction and experience in solving real problems in translational medicine, and it is anticipated that some will lead to innovations with commercial potential. This experience, undertaken by each student as a member of a team and marked by extensive interaction with faculty, peers, and industry partners, enables the student to integrate the leadership and technical dimensions of the professional MTM curriculum.

Rules & Requirements

Prerequisites: Graduate status in the MTM program

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 9-9 hours of independent study per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Letter grade.

Instructors: Li, Song

Objectives & Outcomes

Course Objectives: •
To introduce students to bioengineering research as it is performed at Berkeley and at other institutions
•
To give students opportunities to connect their own work to work in the field overall
•
To give students an opportunity to meet with speakers who can inform and contribute to their post-graduation career paths

Student Learning Outcomes: To introduce students to the breadth of bioengineering research, both here at Berkeley and at other institutions, and help them to connect their work here at Berkeley to the field overall.

Rules & Requirements

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1 hour of seminar per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Offered for satisfactory/unsatisfactory grade only.

Instructor: Faculty

Rules & Requirements

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1-8 hours of directed group study per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Offered for satisfactory/unsatisfactory grade only.

Rules & Requirements

Prerequisites: Graduate standing

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 0 hours of independent study per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Offered for satisfactory/unsatisfactory grade only.

Rules & Requirements

Prerequisites: Graduate standing

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Summer:
6 weeks - 2.5-15 hours of independent study per week
8 weeks - 2-11.5 hours of independent study per week

Additional Details

Subject/Course Level: Bioengineering/Graduate

Grading: Offered for satisfactory/unsatisfactory grade only.

Rules & Requirements

Prerequisites: Graduate standing

Repeat rules: Course may be repeated for credit without restriction.

Hours & Format

Fall and/or spring: 15 weeks - 1 hour of seminar per week

Additional Details

Subject/Course Level: Bioengineering/Professional course for teachers or prospective teachers

Grading: Offered for satisfactory/unsatisfactory grade only.

Instructor: Johnson