Bioengineering

2016-17 General Catalog

Baskin School of Engineering
335 Baskin Engineering Building
(831) 459-2158
https://beng.soe.ucsc.edu/

Faculty

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Program Description

The four concentrations of the UCSC bachelor of science (B.S.) degree in bioengineering prepare graduates for productive employment in industry or further education in graduate school. Each concentration is based on different essential underlying science, but all share an emphasis on teaching engineering design using that basis in science.

The biomolecular engineering concentration is designed for students interested in protein engineering, stem cell engineering, and synthetic biology. The emphasis is on designing biomolecules (DNA, RNA, proteins) and cells for particular functions, and the underlying sciences are biochemistry and cell biology.

The bioelectronics concentration is designed for students interested in the interface between organisms and electronic instrumentation or implants. The emphasis is on the interfacing of biological sensors to computer systems, and the underlying sciences are physics and chemistry.

The assistive technology: motor concentration is designed for students interested in helping people with movement disabilities. The emphasis is on designing exoskeletons and robots, and the underlying sciences are physics and anatomy. 

The assistive technology: cognitive/perceptual concentration is designed for students interested in helping people with cognitive or perceptual disabilities. The emphasis is on designing computer systems that help people compensate for disabilities, and the underlying sciences are psychology and computer science. 

In all four concentrations, students participate in a capstone design experience: a two-quarter group project intended to prepare students for work in industry, a summer full-time synthetic biology project based on the iGEM competition, or a three-quarter senior thesis intended to prepare students for Ph.D. research. All options involve working closely with faculty and other researchers at UCSC, analyzing ideas, developing technologies, and discovering new approaches. Application areas include biomolecular sensors and systems, nano-electronic implants, assistive technologies for the elderly and disabled, bioinformatics, microfluidics, nanoscale biotechnology, environmental monitoring, and other areas at the junction between engineering and the life sciences.

More information about bioengineering research and undergraduate research opportunities can be found on the web at ugr.ucsc.edu, beng.soe.ucsc.edu, cbse.ucsc.edu, biomedical.ucsc.edu, stemdiv.ucsc.edu/marc, and stemdiv.ucsc.edu/ucleads/.

The program is sponsored by the Departments of Biomolecular Engineering, Computer Engineering, Electrical Engineering, and Molecular, Cell, and Developmental Biology, with additional participating faculty in the Departments of Applied Mathematics and Statistics, Chemistry and Biochemistry, and Psychology.

The program has course requirements in mathematics, science, and engineering. Students interested in bioengineering as a major should contact the School of Engineering advising office (advising@soe.ucsc.edu) before enrolling in any courses at UCSC. Early advising is particularly important before choosing calculus and physics courses.

Bioengineering students may continue their research and studies at UCSC in any of several graduate programs. Information may be found at http://www.graddiv.ucsc.edu.

Program Learning Outcomes

A bioengineering student completing the program should:

• have a broad knowledge of science and engineering disciplines including biology, chemistry, physics, mathematics, statistics, and computer science;

• be able to apply their broad knowledge to identify, formulate, and solve engineering design problems;

• be able to find and use information from a variety of sources, including books, journal articles, online encyclopedias, and manufacturer data sheets;

• be able to design and conduct experiments, as well as to analyze and interpret data;

• be able to communicate problems, experiments, and design solutions in writing, orally, and as posters; and

• be able to apply ethical reasoning to make decisions about engineering methods and solutions in a global, economic, environmental, and societal context.

Courses for Nonmajors

The following courses are recommended for nonmajors interested in bioengineering. Computer Engineering 80A, Universal Access: Disability, Technology, and Society; Biomolecular Engineering 80G, Bioethics in the 21st Century: Science, Business, and Society; and Biomolecular Engineering 5, Introduction to Biotechnology. Students are also advised to consult the program discussions of the collaborating departments for additional possibilities related to bioengineering.

Declaration of the Major

To be admitted by the end of the 5th quarter, students need to have taken 50 credits from the following list of courses with a GPA of 2.8 or better:

Applied Mathematics and Statistics (AMS) 7/L, AMS 10, AMS 20, Molecular, Cell, and Developmental Biology (BIOL) 20A, Ecology and Evolutionary Biology (BIOE) 20B, Biomolecular Engineering (BME) 5, BME 51A, BME 51B, BME 80G, Chemistry and Biochemistry (CHEM) 1A, CHEM 1B/M, CHEM 1C/N, CHEM 8A/L, CHEM 8B/M, Computer Engineering (CMPE) 9, CMPE 12/L, CMPE 13/L, CMPE 80A, CMPE 100/L, Computer Science (CMPS) 12A/L, CMPS 12B/M, Mathematics (MATH) 19A, MATH 19B, Physics (PHYS) 5A/L (or 6A/L), PHYS 5B/M (or 6B/M), PHYS 5C/N (or 6C/N), and Psychology (PSYC) 20A.

Students changing majors after the 6th quarter will need to have completed 10 more credits of required courses in the major for each additional quarter past the 6th quarter.

Appeals for major declaration may be filed with the Baskin School of Engineering Office of Undergraduate Affairs by the end of the fifth week of each regular quarter for faculty review. Determinations will be made by the end of the seventh week of the quarter. After the campus major declaration deadline, students submitting an appeal must have a declared alternate major.

Transfer Students

Transfer students need to have completed eight transferable courses from the list used for admission for on-campus students, with a GPA in those courses of 2.8 or better. However, students are recommended to complete at least ten transferable courses prior to transfer, as they may otherwise have difficulty finishing in a timely fashion.

Students may satisfy the bioethics requirement if they have completed a suitable ethics course at their community college, even if the course does not articulate to BME 80G.

Honors in the Major

Bioengineering majors are considered for “Honors in the Major” and “Highest Honors in the Major” based on their GPA and on the results of undergraduate research. Students with a GPA of 3.7 receive “Highest Honors in the Major.” Students with a GPA of 3.3 receive “Honors in the Major.” Students with particularly significant accomplishments in undergraduate research may receive honors or highest honors with a lower GPA. Students who have been found guilty of academic misconduct are not eligible for either honors or highest honors.

Letter Grade Policy

Please refer to the letter grade policy in the School of Engineering section.

Baskin School of Engineering Policies

Please refer to the School of Engineering section of the catalog for additional policies that apply to all Baskin School of Engineering programs.

Materials Fee and Miscellaneous Fees

Please see the section on fees in the School of Engineering section.

Major Requirements

Advising and Elective Approval

Every major must have a bioengineering faculty adviser, assigned by the Baskin School of Engineering undergraduate advising office. With assistance from the adviser, students must formulate a program of proposed course work that meets the major requirements.

Optional Courses for Majors

CMPS 5P, Introduction to Programming in Python, is recommended for those students who have never done computer programming, before taking CMPS 12A, CMPE 12, or BME 160. Python is frequently used in bioengineering jobs, and starting in Python is easier than starting in Java. (The CMPS 5J+11 sequence is permitted, but not recommended for bioengineers.) Biomolecular Engineering 88A, BMES Freshman Design Seminar, is recommended for first-year students interested in learning to think like engineers.  Students considering the assistive technology: motor concentration or desiring an early introduction to the use of mathematics in engineering may wish to take Computer Engineering 8, Robot Automation, in their first quarter.

Courses required for all concentrations (lower-division, 9):

Mathematics 19A-B, Calculus for Science, Engineering, and Mathematics

Biomolecular Engineering 80G, Bioethics in the 21st Century: Science, Business, and Society

Biomolecular Engineering 51A and 51B, Applied Electronics for Bioengineers I and II (students who have previously had) Biomolecular Engineering 101/L, Applied Electronics for Bioengineers, may substitute it for 51A-B)

Chemistry and Biochemistry 1A, 1B/M General Chemistry

Biology (BIOL) 20A, Cell and Molecular Biology

Biology (BIOE) 20B, Development and Physiology

All concentrations also require physics and computer programming, but the details of the requirements differ, due to the different needs of the concentrations (see below).

Courses required for all concentrations (upper-division, 1):

Computer Engineering 185, Technical Writing or Biomolecular Engineering 185, Technical Writing

Capstone requirement, all concentrations, 3 courses

All bioengineering students complete a senior capstone project in bioengineering, either as a group project or as an individual senior thesis doing research in a faculty laboratory. (Satisfies the campus comprehensive requirement.)

Note that the Technical Writing requirement is a prerequisite for all the capstone options, including the senior thesis. The group project courses all have additional prerequisites that may not be met with just the required courses in a concentration. Students are responsible for ensuring that they meet the prerequisites for whichever capstone they choose.

Most students in the Assistive Technology: Cognitive/Perceptual concentration will need to do a senior thesis, because of the number of additional prerequisites they would need to take for any of the group project courses.

Capstone Sequences

Biomolecular Engineering 123A-B, Bioengineering Project; or

Biomolecular Engineering 129A-C, Bioengineering Project; or

Computer Engineering, or Electrical Engineering 129A-C, Capstone Project; (Note: Students may not have all prerequisite courses for 129A-C and will need either an additional course or permission of instructor to enroll); or

BME 180, Professional Practice in Bioengineering (2 credits), and BME 188, Synthetic Biology—Mentored Research (10 credits); or

Fifteen credits of independent study (198), Field Study (193), or senior thesis research (195), in biomolecular engineering, computer engineering, or electrical engineering; and Biomolecular Engineering 123T, Senior Thesis Presentation (2 credits).

Students pursuing the senior thesis option must seek approval of their project one year before graduation, typically spring quarter of the third year. Students spend three or more quarters working on their thesis projects. Thesis students must enroll in 123T, Senior Thesis Presentation, before completing their thesis.

Additional required courses for Biomolecular concentration (16 courses)

Biomolecular Engineering 5, Introduction to Biotechnology

Physics 5A/L or 6A/L, Introduction to Physics I or Introductory Physics I

Physics 5C/N or 6C/N, Introduction to Physics III or Introductory Physics III (the Physics 5 series is recommended; the Physics 6 series is for students changing majors after taking Physics)

Chemistry 1C/N, General Chemistry    

Chemistry 8A/L, Organic Chemistry

Applied Mathematics and Statistics 131, Introduction to Probability Theory

Applied Mathematics and Statistics 132, Classical and Bayesian Inference

One of two three-course sequences in biochemistry or molecular biology. The first sequence is intended for students primarily interested in the design of proteins, while the second is intended for students interested in cellular engineering.

Chemistry 8B/M, Organic Chemistry; Biochemistry and Molecular Biology (BIOC) 100A-B; and Biology (BIOL) 101L, Molecular Biology Laboratory; or

Biology (BIOL) 100, Biochemistry; Biology (BIOL) 101/L, Molecular Biology and Biochemistry Laboratory; and one of Biology 110L, Cell Biology Laboratory; 115L, Eukaryotic Molecular Biology Laboratory; or 120L, Development Laboratory

One of three introductions to programming:

• Computer Science 12A/L, Introduction to Programming/Laboratory; or Computer Science 5J, Introduction to Programming in Java and 11, Intermediate Programming; or Computer Engineering 12/L, Computer Systems and Assembly Language/Laboratory and Computer Engineering 13/L, Computer Systems and C Programming/Laboratory

Biomolecular Engineering 160/L, Research Programming in the Life Sciences

Biomolecular Engineering 110, Bioinformatics Tools

Biology (BIOL) 105, Genetics

One of Biology 110, Cell Biology; Biology 115, Eukaryotic Molecular Biology; or Microbiology and Environmental Toxicology 119, Microbiology.

Design elective from Baskin School of Engineering.

Additional required courses for Bioelectronics concentration (16 courses)

Chemistry 1C/N, General Chemistry

Physics 5A/L, 5B/M, and 5C/N, Introduction to Physics I, II, and III

Applied Mathematics and Statistics 10, Mathematical Methods for Engineers I

Applied Mathematics and Statistics 20, Mathematical Methods for Engineers II

Applied Mathematics and Statistics 131, Introduction to Probability Theory

Applied Mathematics and Statistics 132, Classical and Bayesian Inference

Biomolecular Engineering 140, Bioinstrumentation

Computer Engineering 12/L, Computer Systems and Assembly Language/Laboratory

Computer Engineering 13/L, Computer Systems and C Programming/Laboratory

Computer Engineering 100/L, Logic Design/Laboratory

Electrical Engineering 101/L, Introduction to Electronic Circuits/Laboratory

Electrical Engineering 103/L, Signals and Systems/Laboratory

And two courses from the following:

Computer Engineering 167/L, Sensing and Sensor Technologies/Laboratory or

Electrical Engineering 104, Bio-electronics and Bio-instrumentations or

Electrical Engineering 171/L, Analog Electronics/Laboratory

Additional required courses for Assistive Technology: Motor concentration (16 courses)     

Computer Engineering 80A, Universal Access: Disability, Technology, and Society, or Computer Engineering 8, Robot Automation: Intelligence Through Feedback Control

Physics 5A/L and 5C/N, Introduction to Physics I/Laboratory and Physics III/Laboratory

Computer Engineering 9, Introduction to Statics, Solid Mechanics & Biomechanics

Applied Mathematics and Statistics 10, Mathematical Methods for Engineers I

Applied Mathematics and Statistics 20, Mathematical Methods for Engineers II

Applied Mathematics and Statistics 131, Introduction to Probability Theory

Applied Mathematics and Statistics 132, Classical and Bayesian Inference

Computer Engineering 12/L, Computer Systems and Assembly Language/Laboratory

Computer Engineering 13/L, Computer Systems and C Programming/Laboratory

Computer Engineering 100/L, Logic Design/Laboratory

Microbiology and Environmental Toxicology (METX) 135/L, Functional Anatomy/Laboratory

Computer Engineering 118/L, Introduction to Mechatronics/Laboratory

Electrical Engineering 101/L, Introduction to Electronic Circuits/Laboratory

Electrical Engineering 103/L, Signals and Systems/Laboratory

Computer Engineering 161, Mobile Sensing and Interaction or 167/L, Sensing and Sensor Technologies/Laboratory

Additional required courses for Assistive Technology: Cognitive/Perceptual concentration (15 courses)

Computer Engineering 80A, Universal Access: Disability, Technology, and Society

Physics 5A/L or 6A/L, Introduction to Physics I/Laboratory or Introductory Physics I/Laboratory

Physics 5B/M or 6B/M, Introduction to Physics I/Laboratory or Introductory Physics II/Laboratory

Physics 5C/N or 6C/N, Introduction to Physics III/Laboratory or Introductory Physics

Applied Mathematics and Statistics 10, Mathematical Methods for Engineers I, or Mathematics 21, Linear Algebra

Applied Mathematics and Statistics 7/L, Statistical Methods for the Biological, Environmental, and Health Sciences/Laboratory

One of three introductions to programming:

• Computer Science 12A/L, Introduction to Programming/Laboratory; or

• Computer Science 5J, Introduction to Programming in Java and 11, Intermediate Programming; or

• Computer Engineering 12/L, Computer Systems and Assembly Language/Laboratory and Computer Engineering 13/L, Computer Systems and C Programming/Laboratory

Computer Science 12B/M, Introduction to Data Structures/Laboratory

Computer Science 109, Advanced Programming

Psychology 20A, Cognition: Fundamental Theories

Psychology 100, Research Methods in Psychology

Two upper-division Psychology courses selected from the following:

• Psychology 120, Visual and Spatial Cognition

• Psychology 121, Perception

• Psychology 123, Cognitive Neuroscience

• Psychology 128, Human Factors

• Psychology 129, Human Learning and Memory

Computer Engineering 131, Human Computer Interaction, or CMPM 131, User Experience for Interactive Media

Computer Engineering 161, Mobile Sensing and Interaction

Disciplinary Communication

The Disciplinary Communication requirement is satisfied by the Technical Writing course (CMPE 185 or BME 185) plus the capstone requirement, though oral presentation and writing are integrated throughout the upper-division coursework. The portfolio in the exit requirement is a verification of disciplinary communication in several different forms.

Exit Requirement

Students are required to submit a portfolio, exit survey, and exit interview.

The portfolios must be turned in electronically as PDF files by the last day of the quarter of graduation, and will be reviewed quarterly by the undergraduate director.

Portfolios must contain the following:

• 1) A substantial written report on a design project. This is typically satisfied by a senior thesis, a written capstone project report, or a design report from the Applied Circuits for Bioengineers course.

• 2) Slides from a substantial verbal presentation. This is typically satisfied by a capstone design presentation, Stem Cell Engineering, or other design courses.

• 3) A research poster. This is typically satisfied by a senior thesis poster or a capstone design project poster, presented at the undergraduate poster symposium.

The three parts of the portfolio should represent at least two different design projects. If a senior thesis is completed, it must be provided as the written report.  If a capstone project is completed, it must be provided as one (or more) of the three submissions.

Exit interviews are scheduled during the last week of the quarter by the Baskin School of Engineering (BSOE) advising office, generally as small group interviews.

Bioengineering Major Planners

The following sample academic plans show possible courses of study for a bioengineering major. The first plan follows the biomolecular engineering concentration, the second the bioelectronics concentration, the third the assistive technology: motor concentration, and the fourth the assistive technology: cognitive/perceptual concentration. 

All plans assume that students are ready for calculus and advanced computer programming courses when they start. Those who need to take precalculus CMPS 5P. or CMPS 5J may not be able to complete the entire program within four years.

Students should consider taking courses during the summer to ensure timely completion of the degree. Courses planned to be taken at institutions other than UCSC require pre-approval by the undergraduate director.

All students should meet quarterly with an adviser from the School of Engineering Undergraduate Advising Office to review their finished and planned courses, as schedules and prerequisites change frequently. Any electives should be chosen well ahead of time, to ensure that prerequisites can be scheduled.

Plan One (biomolecular engineering)

Year	Fall	Winter	Spring
1st (frosh)	college core	BME 5	gen ed (C2)
	MATH 19A	MATH 19B	BIOL 20A
	CHEM 1A	CHEM 1B/M	CHEM 1C/N
		BME 88A
2nd (soph)	BME 80G	gen ed	PHYS 5C/N
	PHYS 5A/L	BIOE 20B	BIOL 105
	CHEM 8A/L	CHEM 8B/M	BME 160/L
3rd (jr)	BIOC 100A	BIOC 100B	BME 51B
	CMPS 12A/L	BME 185	BIOL 110
	BME 110	BIOL 101L
		BME 51A
4th (sr)	BME 195	BME 195	BME 195
	AMS 131	AMS 132	BME 128/L
		BME 123T	gen ed

Plan Two (bioelectronics)

Year	Fall		Winter		Spring
1st (frosh)	college core		CMPE 12/L		CMPE 13/L
	MATH 19A		MATH 19B		BME 51B
	PHYS 5A/L		BME 51A		PHYS 5C/N
2nd (soph)	CHEM 1A		CHEM 1B/M		CHEM 1C/N
	AMS 10		AMS 20		gen ed (C2)
	BME 80G		EE 101/L		CMPE 100/L
3rd (jr)	BIOL 20A		PHYS 5B/M		EE 171/L
	EE 103/L		CMPE 167/L		CMPE 185
	CMPE 121/L		BIOE 20B		gen ed
4th (sr)	EE 129A		EE129B		EE 129C
	BME 140		AMS 132		gen ed
	AMS 131		gen ed

Plan Three (assistive technology: motor)

Year	Fall	Winter	Spring
1st (frosh)	college core	gen ed (C2)	CMPE 80A
	MATH 19A	MATH 19B	BME 51B
	PHYS 5A/L	BME 51A	PHYS 5C/N
2nd (soph)	BME 80G	AMS 20	CMPE 100/L
	CMPE 12/L	CMPE 13/L	gen ed
	AMS 10	CMPE 9
3rd (jr)	EE 101/L	AMS 132	EE 103/L
	CHEM 1A	CHEM 1B/M	BIOL 20A
	AMS 131	CMPE 185
4th (sr)	CMPE 129A	CMPE 129B	CMPE 129C
	CMPE 118/L	CMPE 167/L	gen ed
	BIOE 20B		METX 135/L

Plan four (assistive technology: cognitive/perceptual)

Year	Fall	Winter	Spring
1st (frosh)	college core	gen ed (C2)	CMPE 80A
	MATH 19A	MATH 19B	AMS 10
	PHYS 5A/L	PHYS 5B/M	PHYS 5C/N
2nd (soph)	CHEM 1A	CHEM 1B/M	BIOL 20A
	BME 80G	CMPS 12A/L	CMPS 12B/M
	AMS 7/L	PSYC 100
3rd (jr)	PSYC 20A	PSYC 120	PSYC 128
	BIOE 20B	BME 51A	CMPS 109
	gen ed	CMPE 161	BME 51B
4th (sr)	BME 195	BME 195	BME 195
	CMPE 185	BME 123T	gen ed
		CMPM 131

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Revised: 09/01/16