Biomolecular Engineering and Bioinformatics B.S.

Information and Policies

Introduction

The biomolecular engineering and bioinformatics major includes the biomolecular engineering (BME) and bioinformatics (BINF) concentrations. The BME 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 BINF concentration combines mathematics, science, and engineering to explore and understand biological data from high-throughput experiments, such as genome sequencing, gene-expression chips, and proteomics experiments. The program builds upon the research and academic strengths of the faculty in the Biomolecular Engineering Department.

In both concentrations, students participate in a capstone experience. Options for the senior capstone experience include

• Senior Design—a three-quarter group project intended to prepare students for work in industry,
• iGEM -- a three-quarter, team-oriented, synthetic biology project (including summer, based on the international iGEM competition,
• a three-quarter Senior thesis,
• or an Advanced bioinformatics course series. The last option is the required capstone for students participating in the bioinformatics concentrations.

All capstone 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 at Undergraduate Research Opportunities, the Genomics Institute, the Program in Biomedical Sciences and Engineering, the STEM Maximizing Access to Research Careers (MARC) program, and the STEM diversity programs.

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

Biomolecular engineering and bioinformatics students may continue their research and studies at UCSC in any of several graduate programs. Information may be found at the Division of Graduate Studies website.

The immense growth of biological information stored in computerized databases has led to a critical need for people who can understand the languages, tools, and techniques of statistics, science, and engineering. A classically trained scientist may be unfamiliar with the statistical and algorithmic knowledge required in this field. A classically trained engineer may be unfamiliar with the chemistry and biology required in the field. Thus, this major strives for a balance of the two: an engineer focused on the problems of the underlying science or, conversely, a scientist focused on the use of engineering tools for analysis and discovery.

Program Learning Outcomes

A biomolecular engineering and bioinformatics student completing the program should:

• have a broad knowledge of science and engineering disciplines including biology, chemistry, mathematics, statistics, and computer science; those completing the BINF concentration will also have a detailed knowledge of mathematics, statistics, and computer science; and, those completing the BME concentration will have broader knowledge in biology and chemistry;
• be able to apply their knowledge to identify, formulate, and solve engineering design problems;
• be able to write programs in Python;
• 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 work effectively with partners and on teams;
• 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.

Academic Advising for the Program

The Baskin Engineering Undergraduate Advising office offers general advising for prospective and declared undergraduates majoring in Baskin Engineering programs. The office handles major declarations, transfer credits, course substitutions, articulations, and degree certifications. Undergraduate students obtain and submit all paperwork requiring departmental approval to the undergraduate advising office. Transfer students should also refer to the Transfer Information and Policy section.

Baskin Engineering Building, Room 225
bsoeadvising@ucsc.edu
(831) 459-5840

Getting Started in the Major: Frosh

This is a course-intensive and/or sequential program, and students who intend to pursue this major must begin taking classes for the major in their first year at the University of California, Santa Cruz. Timely completion of the degree will require completion of a general Chemistry series (CHEM 3, or CHEM 4) and Engineering Calculus ( MATH19) during the first year. Math placement is required for one or more of the foundational courses for this major. For more information, please review the Math Placement website.

Transfer Information and Policy

Transfer Admission Screening Policy

Transfer students need to complete the equivalents of eight courses from the following list with a GPA in those courses of 2.8 or better:

Although not required for admission, transfer students are strongly recommended to complete at least ten courses from the above list if they wish to graduate in two years. Completion of the Organic Chemistry requirements before transfer is especially important.

Students with fewer than 10 transferable courses will find it difficult to complete the major in only two more years.

Prospective students are encouraged to prioritize required and recommended major preparation, and may additionally complete courses that articulate to UC Santa Cruz general education requirements as time allows.

Transferring to Biomolecular Engineering

Students transferring into the biomolecular engineering concentration may also count any of the following:

Transferring to Bioinformatics

The following courses are recommended to be taken before transfer, and will count toward transfer screening:

Getting Started in the Major: Transfer Students

Successful transition to UC Santa Cruz happens with early advisor contact, preparing and submitting course descriptions for articulation purposes, and taking summer session courses prior to their first fall quarter. Specific information for transfer students can be found at the Baskin Engineering Transfer webpage. Transfer students should declare their major during their first quarter at UCSC; instructions for declaring a major at Baskin Engineering are on the major declaration webpage.

Major Qualification Policy and Declaration Process

Major Qualification

In order to be admitted into the biomolecular engineering and bioinformatics major students must be listed as a proposed major within Baskin Engineering. Please refer to Baskin Engineering's "Prospective Students", "Admitted Students" and its "Current Students" sections in the catalog and the Undergraduate Affairs website for more information.

In addition to being listed as a proposed Baskin Engineering major, students must have completed at least 45 credits with a GPA of 2.8 or better in courses required for the major. Students with more than 7 credits of grades of NP, C-, D+, D, D-, or F in these courses are not qualified for the major.

Declaration of the major can happen no sooner than the student's second quarter, and must precede class enrollment for the student’s third year (see below: How to Declare a Major). Students wishing to declare the biomolecular engineering and bioinformatics major after the sixth quarter must appeal, must already have a declared major in which they have completed at least one major requirement course and be making reasonable progress, and must have completed 10 more credits of required courses in the biomolecular engineering and bioinformatics major for each additional quarter.

Transfer students should refer to the Transfer Information and Policy section.

Appeal Process

Students may appeal a major qualification decision by filing a petition with Baskin Engineering Advising. The appeal process is described at the Baskin Engineering Undergraduate Affairs website.

If you have further questions concerning the appeal process, please contact the Undergraduate Advising office at (831) 459-5840 or email bsoeadvising@ucsc.edu.

How to Declare a Major

Instructions for declaring a major in Baskin Engineering are on the division's website here.

Letter Grade Policy

Baskin Engineering requires letter grades for all courses in an engineering major.

Course Substitution Policy

Please refer to the Undergraduate Affairs Policies, Forms and Petitions website for Baskin Engineering policies about substitutions and taking courses at other institutions after enrolling at UC Santa Cruz.

Double Majors and Major/Minor Combinations Policy

Due to course overlap between the biomolecular engineering and bioinformatics (BMEB) B.S., the biotechnology B.A., and the bioinformatics minor, none of these double major or major/minor combinations will be considered. Other major/minor combinations are permitted and encouraged. Double majors with the biotechnology B.A. and majors in the Humanities, Social Sciences or Arts Divisions are specifically encouraged.

Study Abroad

Students are encouraged to investigate studying for short periods of time (a summer or a quarter) at other institutions, to broaden their education. Proposed plans of study should still be cleared with the undergraduate director.

Honors

Biomolecular engineering and bioinformatics majors are considered for "Honors in the Major" and "Highest Honors in the Major" based on their GPA and on results of undergraduate research. Students with a GPA of 3.7 or higher receive "Highest Honors in the Major." Students with a GPA of 3.3 or higher, but lower than 3.7, 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.

Because of the enormous breadth of requirements, biomolecular engineering and bioinformatics majors are urged to take honors courses or sections to get as much as possible out of the courses they take in each field.

Biomolecular Engineering Concentration

The biomolecular engineering concentration focuses on wet-lab work, but with a modern appreciation for the statistics and computational tools needed for high-throughput experimentation.

Course Requirements

Biomolecular engineering concentration majors must complete the following courses:

Lower-Division Courses

Biology

Bioethics

Chemistry

Select one of the following General Chemistry series:

Organic Chemistry

All of the following courses:

Laboratory Training

All of the following courses:

Mathematics

Choose one of the following options:

Applied Math

Both of these applied math courses:

Physics

All of the following courses:

Upper-Division Courses

Statistics

Two statistics courses (note: STAT 132 is a prerequisite for CSE machine learning courses):

Biochemistry and Molecular Biology

All of the following courses:

Biomolecular Engineering

Choose one of the following courses:

Plus all of the following courses:

Plus one of the following Modeling/Design sequences:

Technical Writing (one of the following courses)

Elective

One of the following (the course taken to satisfy this elective cannot be used to satisfy other requirements of the major):

Disciplinary Communication (DC) Requirement

Students of every major must satisfy that major's upper-division Disciplinary Communication (DC) requirement. Biomolecular engineering and bioinformatics majors satisfy the DC requirement by completing one of the following courses:

Comprehensive Requirement

All biomolecular engineering concentration students must complete a senior capstone project as a group project, as a series of Advanced Bioinformatics courses, or as an individual senior thesis doing research in a faculty laboratory.

Note that the Technical Writing requirement is a prerequisite for all the capstone options, including the senior thesis. Students pursuing the senior thesis option must write a two-page thesis proposal and seek approval of their project from the undergraduate director in the quarter preceding the independent study courses, typically spring quarter of the third year. Students are responsible for ensuring that they meet the prerequisites for whichever capstone they choose.

To complete the senior capstone requirement, Biomolecular Engineering concentrations students must complete one of the following:

The thesis option consists of 15 credits of Independent Study (BME 198), 15 credits of Field Study (BME 193), or 15 credits of Senior Thesis Research (BME 195) in biomolecular engineering.

Students pursuing the senior thesis option must write a two-page thesis proposal and seek approval of their project from the undergraduate director in the quarter preceding the independent study courses, typically spring quarter of the third year.

Exit Requirements

Students are required to submit a portfolio, exit survey, and attend an 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:

• A substantial written report on a modeling/design project. This is typically satisfied by a senior thesis, or a written capstone project report.
• Slides from a substantial verbal presentation. This is typically satisfied by a capstone design presentation, Stem Cell Engineering, or other design courses.
• 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 Baskin Engineering advising office, generally as small group interviews.

Planners

The tables below are for informational purposes and do not reflect all university, general education, and credit requirements. See Undergraduate Graduation Requirements for more information.

Every biomolecular engineering and bioinformatics major must have a faculty advisor, assigned by Baskin Engineering's undergraduate advising office, and with that advisor must formulate a program of proposed coursework that meets the major requirements. The choice of capstone and electives should be made early, so that the plan can be tailored to fit in the chosen courses.

As in all engineering and science programs, it is recommended that students spread their general education requirements out over all 12 quarters. Delaying a general education requirement is safer than delaying a major requirement.

It is recommended that students reserve the summer after the junior year for undergraduate research.

Curriculum charts for the major are available on the BSOE website.

Sample Plan: Biomolecular Engineering Concentration

* WRIT 2 should be taken in or before spring quarter of the second year.

Students who can take Organic Chemistry (CHEM 8A and CHEM 8B, or transferable equivalents) in summer after their first year can take BIOC 100A in their second year and be ready to join a research lab a year earlier. Here is an alternative plan for students who do organic chemistry in summer.

Sample Plan: Biomolecular Engineering Concentration (CHEM 8A & CHEM 8B In summer after first year)

* WRIT 2 should be taken in or before spring quarter of the second year.

General education requirements:

CC, ER, and IM are not met by any courses in the program.

MF, SI, SR and PE are met by required courses.

TA can be met by several electives: BME 122H, BME 132, BME 177, or BME 178.

PR-E can be met by some capstone options: BME 129C or BME 180.

C is not met by courses in the program, but is a prerequisite for the required BME 185 or CSE 185E course.

Transfer planner

This transfer planner assumes that a student has completed the equivalent of CHEM 3A, CHEM 3B, CHEM 3BL, CHEM 3C, CHEM 3CL, CHEM 8A, CHEM 8B, MATH 19A, MATH 19B, PHYS 5A, PHYS 5L, BIOL 20A, AM 10, a molecular biology lab, and all general education courses before coming to UC Santa Cruz. Students are also expected to have completed all the general education requirements, except those covered by the required courses. This planner is only a proof-of-concept that the major can be completed in another two years; each student will need to work with an advisor to tailor their own schedule.

Bioinformatics Concentration

The bioinformatics concentration focuses on dry-lab (computational) techniques.

Bioinformatics concentration majors must complete the following courses:

Course Requirements

Lower-Division Courses

Biology

Biomolecular Engineering

Chemistry

All of the following courses:

Organic Chemistry

All of the following courses:

Computer Science and Engineering

All of the following courses:

Mathematics

Choose one of the following options:

Upper-Division Courses

Statistics

Two statistics courses (note: STAT 132 is a prerequisite for CSE Machine Learning courses):

Biochemistry and Molecular Biology

Biomolecular Engineering

Plus one of the following courses:

Plus all of the following courses:

Plus one of the following Modeling/Design sequences:

Technical Writing

Choose one of the following courses:

Elective

One of the following (courses satisfying an elective cannot be used to satisfy other requirements of the major):

Database management

The following course is required:

Disciplinary Communication (DC) Requirement

Students of every major must satisfy that major's upper-division Disciplinary Communication (DC) requirement. BMEB majors satisfy the DC requirement by completing one of the following courses:

Comprehensive Requirement

The senior capstone is fulfilled by completing all of the following courses:

Exit Requirements

Students are required to submit a portfolio, exit survey, and attend an 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:

• A substantial written report on a modeling/design project. This is typically satisfied by a written capstone project report.
• Slides from a substantial verbal presentation. This is typically satisfied by a capstone design presentation, Stem Cell Engineering, or other design courses.
• A research poster. This is typically satisfied by 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 Engineering advising office, generally as small group interviews.

Planners

The tables below are for informational purposes and do not reflect all university, general education, and credit requirements. See Undergraduate Graduation Requirements for more information.

Every biomolecular engineering and bioinformatics major must have a faculty advisor, assigned by the Baskin Engineering undergraduate advising office, and with that advisor must formulate a program of proposed coursework that meets the major requirements. The choice of capstone and electives should be made early, so that the plan can be tailored to fit in the chosen courses.

As in all engineering and science programs, it is recommended that students spread their general education requirements out over all 12 quarters. Delaying a general education requirement is safer than delaying a major requirement.

It is recommended that students reserve the summer after the junior year for undergraduate research.

Curriculum charts for the major are available on the BSOE website.

Sample Plan: Bioinformatics Concentration

* WRIT 2 should be taken in or before spring quarter of the second year.

General education requirements:

CC, ER, IM, and PR-E are not met by any courses in the program.

MF, PE-T, SI, and SR are met by required courses.

TA can be met by several electives: BME 122H, BME 132, BME 177, or BME 178.

C is not met by courses in the program, but is a prerequisite for the required BME 185 or CSE 185E course.

Transfer planner

This transfer planner assumes that a student has completed the equivalent of CHEM 3A, CHEM 3B, CHEM 3BL, CHEM 3C, CHEM 3CL, CHEM 8A, CHEM 8B, MATH 19A, MATH 19B, BIOL 20A, CSE 16, and CSE 30 and all general education requirements, except those covered by the required courses. This planner is only a proof-of-concept that the major can be completed in another two years; each student will need to work with an advisor to tailor their own schedule.