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,
  • a summer full-time synthetic biology project based on the 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 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.

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.

Academic Advising for the Program

The Baskin School of Engineering Undergraduate Advising office offers general advising for prospective and declared undergraduates majoring in School of 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
advising@soe.ucsc.edu
(831) 459-5840

Getting Started in the Major

Students applying for admission as first-year students proposing to take the biomolecular engineering and bioinformatics major should have completed four years of high school mathematics (through advanced algebra and trigonometry) and three years of science, including one year of chemistry and one year of biology. Comparable college mathematics and science courses completed at other institutions may be accepted in place of high school preparation. Students without this preparation may be required to take additional courses to prepare themselves for the program.

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 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 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.

Major Qualification Policy and Declaration Process

Major Qualification

In order to be admitted into the Bioinformatics major students must be listed as a proposed major within the School of Engineering. Please refer to the School of Engineering's "Proposed Engineering Major Status" and its "Declaring a School of Engineering Major" sections in the catalog and the Undergraduate Affairs website for more information.

In addition to being listed as a proposed School of Engineering major, students must have completed at least 50 credits with a GPA of 2.8 or better in courses required for the major. Students with two or more grades of NP, C-, D+, D, D-, or F in these courses are not qualified to declare.

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 who are informed that they are not eligible to declare may appeal this decision by submitting a letter to the undergraduate director within 15 days from the date the notification was mailed. Within 15 days of receipt of the appeal, the Undergraduate Advising office will notify the student, the college, and the Office of the Registrar of the decision.

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

More information regarding the appeal process can be found here: https://undergrad.soe.ucsc.edu/appeal-your-major

How to Declare a Major

Instructions for declaring a major in the Baskin School of Engineering are at https://undergrad.soe.ucsc.edu/declare-your-major.

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:

CSE13SComputer Systems and C Programming

7

CSE16Applied Discrete Mathematics

5

CSE182Introduction to Database Management Systems

5

BME80G
/PHIL 80G
Bioethics in the 21st Century: Science, Business, and Society

5

CHEM1AGeneral Chemistry

5

CHEM1BGeneral Chemistry

5

CHEM1CGeneral Chemistry

5

CHEM8AOrganic Chemistry

5

CHEM8BOrganic Chemistry

5

BIOE20BDevelopment and Physiology

5

BIOL20ACell and Molecular Biology

5

MATH19ACalculus for Science, Engineering, and Mathematics

5

MATH19BCalculus for Science, Engineering, and Mathematics

5

PHYS5AIntroduction to Physics I

5

BME21LIntroduction to Basic Laboratory Techniques

5

CSE 13S, CSE 16 and CSE 182 are only relevant for the bioinformatics concentration in the major; BIOE 20B, BME 21L and PHYS 5A are only relevant for the biomolecular engineering concentration in the major.

Transfer students with a articulated ethics course may count it, even if it is not bioethics and the course is not articulated to BME 80G. 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.  Students with fewer than 10 transferable courses may find it difficult to complete the major in only two more years.

Getting Started at UCSC as a Transfer Student

Transfer students should declare their major in their first quarter at UCSC. Instructions for declaring a major in the Baskin School of Engineering are at https://undergrad.soe.ucsc.edu/declare-your-major.

Letter Grade Policy

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

Course Substitution Policy

Please refer to the Undergraduate Affairs course substitution website for Baskin School of Engineering policies about taking courses at other institutions after enrolling at UCSC.

Double Majors and Major/Minor Combinations Policy

Double majors with other biology-related majors are permitted for the bioinformatics concentration, but not for the biomolecular engineering concentration.

The BMEB major cannot be combined with a bioinformatics minor.

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.

The BME Department has established an exchange program with Danish Technical University (DTU), which makes study there for one semester relatively easy, particularly for the bioinformatics concentration. Proposed plans of study should still be cleared with the undergraduate director.

Other exchange programs are also being developed.

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 whenever possible 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

All of the following courses:

BIOL20ACell and Molecular Biology

5

BIOE20BDevelopment and Physiology

5

Biology laboratory course

Either of the following courses:

BIOL20LExperimental Biology Laboratory

2

BME21LIntroduction to Basic Laboratory Techniques

5

BME 21L is strongly preferred.

Biomolecular Engineering
All of the following courses:
BME51AApplied Electronics for Bioengineers Part 1

5

BME51BApplied Electronics for Bioengineers Part 2

5

BME80G
/PHIL 80G
Bioethics in the 21st Century: Science, Business, and Society

5

Chemistry

All of the following courses:

CHEM1AGeneral Chemistry

5

CHEM1BGeneral Chemistry

5

CHEM1MGeneral Chemistry Laboratory

2

CHEM1CGeneral Chemistry

5

CHEM1NGeneral Chemistry Laboratory

2

CHEM8AOrganic Chemistry

5

CHEM8BOrganic Chemistry

5

Laboratory courses

One of the following options:

Either these courses

BME22LFoundations of Design and Experimentation in Molecular Biology, Part I

2

BME23LFoundations of Design and Experimentation in Molecular Biology, Part II

2

or these courses

CHEM8LOrganic Chemistry Laboratory

2

CHEM8MOrganic Chemistry Laboratory

2

BME 22L and BME 23L strongly preferred

Mathematics

Choose one of the following options:

Either these courses

MATH20AHonors Calculus

5

MATH20BHonors Calculus

5

or these courses

MATH19ACalculus for Science, Engineering, and Mathematics

5

MATH19BCalculus for Science, Engineering, and Mathematics

5

MATH 19A and MATH 19B are the recommended sequence. Credit for one or both can be granted with adequate performance on the College Entrance Examination Board (CEEB) calculus AB or BC Advanced Placement examination. 

Physics

Choose one of the following options:

Either these courses

PHYS5AIntroduction to Physics I

5

PHYS5LIntroduction to Physics Laboratory

1

or these courses

PHYS6AIntroductory Physics I

5

PHYS6LIntroductory Physics Laboratory

1

PHYS 5A and PHYS 5L are strongly recommended.

Upper-Division Courses

Statistics

All of the following courses:

STAT131Introduction to Probability Theory

5

STAT132Classical and Bayesian Inference

5

Students may petition to substitute STAT 206 for STAT 132.

Biochemistry and Molecular Biology

All of the following courses:

BIOC100ABiochemistry and Molecular Biology

5

BIOC100BBiochemistry and Molecular Biology

5

Biomolecular Engineering
Choose one of the following courses:
BME105Genetics in the Genomics Era

5

BIOL105Genetics

5

BME 105 is strongly recommended.

Plus all of the following courses:
BME110Computational Biology Tools

5

BME160Research Programming in the Life Sciences

6

BME163Applied Visualization and Analysis of Scientific Data

5

Plus one of the following design-elective courses:
BME128Protein Engineering

5

BME140Bioinstrumentation

5

BME177Engineering Stem Cells

5

Technical Writing (one of the following courses)
BME185Technical Writing for Biomolecular Engineers

5

CSE185ETechnical Writing for Computer Engineers

5

BME 185 is recommended, as CSE 185E has additional prerequisites.

Electives

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

BIOL115Eukaryotic Molecular Biology

5

METX119Microbiology

5

BIOC100CBiochemistry and Molecular Biology

5

BME122HExtreme Environmental Virology

5

BME128Protein Engineering

5

BME128LProtein Engineering Laboratory

2

BME130Genomes

5

BME132Evolutionary Genomics

5

BME140Bioinstrumentation

5

BME177Engineering Stem Cells

5

BME178Stem Cell Biology

5

or any 5-credit biomolecular engineering graduate course

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:

BME185Technical Writing for Biomolecular Engineers

5

CSE185ETechnical Writing for Computer Engineers

5

BME 185 is recommended, as CSE 185E has additional prerequisites.

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:

Either these courses

BME129AProject Design and Implementation in Biomolecular Engineering I

5

BME129BProject Design and Implementation in Biomolecular Engineering II

5

BME129CProject Design and Implementation in Biomolecular Engineering III

5

or these courses

BME180Professional Practice in Bioengineering

2

BME188ASynthetic Biology--Mentored Research A

5

BME188BSynthetic Biology--Mentored Research B

5

or these courses

BME205Bioinformatics Models and Algorithms

5

BME230AIntroduction to Computational Genomics and Systems Biology

5

or these courses

BME193Field Study

5

BME123TSenior Thesis Writing

5

or these courses

BME195Senior Thesis Research

5

BME123TSenior Thesis Writing

5

or these courses

BME198Individual Study or Research

5

BME123TSenior Thesis Writing

5

The thesis option consists of 12 credits of Independent Study (BME 198). Field Study (BME 193), or Senior Thesis Research (BME 195) in biomolecular engineering; and BME 123T, Senior Thesis Presentation, 5 credits.

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 spend three or more quarters working on their thesis projects. Thesis students must enroll in BME 123T, Senior Thesis Presentation, before completing their thesis.

Planners

Every biomolecular engineering and bioinformatics major must have a faculty adviser, assigned by the Baskin School of Engineering undergraduate advising office, and with that adviser must formulate a program of proposed coursework that meets the major requirements.

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.

Four-year plans require individual design to fit in the desired electives. It is recommended that students reserve the summer after the junior year for undergraduate research.

Curriculum charts for the major are available here.

Sample Plan: Biomolecular Engineering Concentration

Year Fall Winter Spring
1st (frosh) CHEM 1A
MATH 19A MATH 19B
  CHEM 1B & CHEM 1M CHEM 1C & CHEM 1N
    BME 21L
2nd (soph) PHYS 5A & PHYS 5L BME 51A BME 51B
BME 22L
BME 23L
BME 105
CHEM 8A CHEM 8B  
BIOL 20A BIOE 20B  
3rd (junior) BIOC 100A BIOC 100B Design elective
BME 110 BME 160  BME 163
BME 185    
4th (senior) BME 129A BME 129B BME 129C
STAT 131 STAT 132 Elective
BME 80G    

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)

Year Fall Winter Spring
1st (frosh) CHEM 1A
MATH 19A
BIOL 20A
  CHEM 1B & CHEM 1M CHEM 1C & CHEM 1N
    BME 21L
2nd (soph) BIOE 20B
PHYS 5A & PHYS 5L MATH 19B
BME 22L BME 23L BME 105
BIOC 100A BIOC 100B  
     
3rd (junior) BME 185 BME 51A BME 51B
BME 110 BME 160  BME 163
BME 80G   Design elective
4th (senior) BME 129A BME 129B BME 129C
STAT 131 STAT 132 Elective
     

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

Year Fall Winter Spring
1st (junior) BIOC 100A BIOC 100B
BME 105
BME 185 BME 110
BME 163
  BME 160
Design elective
BME 22L
BME 23L  
2nd(senior) BME 129A BME 129B BME 129C
STAT 131 STAT 132 Elective
BME 80G BME 51A
BME 51B

This transfer planner assumes that a student has completed the equivalent of CHEM 1A, CHEM 1B, CHEM 1M, CHEM 1C, CHEM 1N, CHEM 8A, CHEM 8B, MATH 19A, MATH 19BPHYS 5A, PHYS 5L, BIOL 20ABIOE 20B, and BME 21L before coming to UCSC. Students are also expected to have completed all the general education requirements, expect those covered by the required courses.

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

The following course:

BIOL20ACell and Molecular Biology

5

Biomolecular Engineering

The following course:


BME80G
/PHIL 80G
Bioethics in the 21st Century: Science, Business, and Society

5

Chemistry

All of the following courses:

CHEM1AGeneral Chemistry

5

CHEM1BGeneral Chemistry

5

CHEM1MGeneral Chemistry Laboratory

2

CHEM1CGeneral Chemistry

5

CHEM1NGeneral Chemistry Laboratory

2

CHEM8AOrganic Chemistry

5

CHEM8BOrganic Chemistry

5

Computer Science and Engineering

All the following courses

 

CSE16Applied Discrete Mathematics

5

CSE13SComputer Systems and C Programming

7

Note: BME 160 needs to be before CSE 13S.

Mathematics
Choose one of the following options:
Either these courses

MATH20AHonors Calculus

5

MATH20BHonors Calculus

5

or these courses

MATH19ACalculus for Science, Engineering, and Mathematics

5

MATH19BCalculus for Science, Engineering, and Mathematics

5

MATH 19A and MATH 19B are the recommended sequence. Credit for one or both can be granted with adequate performance on the College Entrance Examination Board (CEEB) calculus AB or BC Advanced Placement examination. 

Upper-Division Courses

Statistics

All of the following courses:

STAT131Introduction to Probability Theory

5

STAT132Classical and Bayesian Inference

5

Students may petition to substitute STAT 206 for STAT 132.

Biochemistry and Molecular Biology
BIOC100ABiochemistry and Molecular Biology

5

Biomolecular Engineering
Plus one of the following courses:
BME105Genetics in the Genomics Era

5

BIOL105Genetics

5

BME 105 is strongly recommended.

Plus all of the following courses:
BME110Computational Biology Tools

5

BME160Research Programming in the Life Sciences

6

BME163Applied Visualization and Analysis of Scientific Data

5

Technical Writing

Choose one of the following courses:

BME185Technical Writing for Biomolecular Engineers

5

CSE185ETechnical Writing for Computer Engineers

5

CSE 185E is recommended, as BME 185 has additional wet-lab prerequisites.

Electives

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

BME122HExtreme Environmental Virology

5

BME128Protein Engineering

5

BME128LProtein Engineering Laboratory

2

BME130Genomes

5

BME132Evolutionary Genomics

5

BME140Bioinstrumentation

5

BME177Engineering Stem Cells

5

BME178Stem Cell Biology

5

CSE142Machine Learning

5

or any 5-credit biomolecular engineering graduate course

BME 230B is strongly recommended as the elective. CSE 142 has additional prerequisites.

Database management

The following course is required:

CSE182Introduction to Database Management Systems

5

CSE 180 may be substituted for CMPS 182, but additional prerequisites would be required.

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:

BME185Technical Writing for Biomolecular Engineers

5

CSE185ETechnical Writing for Computer Engineers

5

CSE 185E is recommended, as BME 185 has additional wet-lab prerequisites.

Comprehensive Requirement

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

BME205Bioinformatics Models and Algorithms

5

BME230AIntroduction to Computational Genomics and Systems Biology

5

Planners

Every biomolecular engineering and bioinformatics major must have a faculty adviser, assigned by the Baskin School of Engineering undergraduate advising office, and with that adviser must formulate a program of proposed coursework that meets the major requirements.

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.

Four-year plans require individual design to fit in the desired electives. It is recommended that students reserve the summer after the junior year for undergraduate research.

Curriculum charts for the major are available here.

Sample Plan: Bioinformatics Concentration

Year Fall Winter Spring
1st (frsh)   MATH 19A MATH 19B
CHEM 1A CHEM 1B & CHEM 1M CHEM 1C & CHEM 1N
     
2nd (soph) CHEM 8A CHEM 8B BIOL 20A
BME 80G BME 160 BME 105
  CSE 16
CSE 13S
3rd (junior) BIOC 100A CSE 185E CSE 182
STAT 131 STAT 132 BME 163
BME 110    
4th (senior) BME 205 BME 230A BME 230B
     
     

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

Year  Fall Winter  Spring 
3rd
(junior)
BIOC 100A BME 110 BME 105
  BME 160 BME 163
STAT 131 STAT 132 CSE 185E
4th
(senior)

BME 205 BME 230A BME 230B
BME 80G   CSE 182
     

This transfer planner assumes that a student has completed the equivalent of CHEM 1A, CHEM 1B, CHEM 1M, CHEM 1C, CHEM 1N, CHEM 8A, CHEM 8B, MATH 19A, MATH 19B, BIOL 20A, CSE 16, and CSE 13S before coming to UCSC.  Students are expected to have completed all but four of the general education requirements.