Biomolecular Engineering and Bioinformatics B.S.

• Information and Policies
• Biomolecular Engineering Concentration
• Bioinformatics Concentration

Information and Policies

Introduction Expand and Collapse

The Biomolecular Engineering and Bioinformatics (BMEB) Bachelor of Science 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 BMEB major builds upon the research and academic strengths of the faculty in the Biomolecular Engineering Department.

The BMEB B.S. 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 ([e-mail]) before enrolling in any courses at UCSC. Early advising is particularly important before choosing calculus and physics courses.

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

Capstone option 1: Series of project-based engineering design courses taken in the senior year where students propose and execute a design project, and then present their work through presentations and a capstone report. Two series are available:

(1) Advanced bioinformatics individual capstone project: Series of three courses taken in the senior year: BME 205 (fall), BME 230A (winter), and BME 129C (spring). Note: students are expected to present their work and complete a capstone report in BME 129C based on the project they started in BME 205 and BME 230A.

or

(2) Biomolecular engineering team design project: Series of three courses taken in the senior year: BME 129A (fall), BME 129B (winter), and BME 129C (spring). Ideal for students interested in working in industry. Note: students are expected to present their work and complete a capstone report in BME 129C based on the project they started in BME 129A and BME 129B. Presentations and capstone report are completed as a team.

Capstone option 2: Individual senior thesis.

Timeline: Students should identify a faculty to serve as their capstone mentor and begin working in the research lab before the student's senior year. Note: many faculty expect students to work in the lab prior to senior year, including the summer before senior year. Students must submit a project proposal in late summer or in the first two weeks of fall quarter of their senior year to the Undergraduate Program Director Dr. Dianne Hendricks.

Senior thesis research consists of 15 credits of Senior Thesis Research (BME 195). 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 first quarter of BME 195, typically summer quarter before senior year. Students typically complete 15 credits of BME 195 during their senior year as follows: 5 credits per quarter fall/winter/spring.

Capstone option 3: iGEM (international Genetically Engineered Machines)

Students complete a team-oriented, student-led synthetic biology project based on the international iGEM competition. Students interested in the UCSC iGEM team should contact the iGEM faculty mentor (contact information can be obtained from the undergraduate program director.) This capstone option is available only to BMEB B.S. majors in the Biomolecular concentration.

Timeline: Students interested in iGEM complete a written application and interview in fall of their junior year. Students selected for the team enroll in two courses in junior year: BME 180 (winter) and BME 188A (spring) and two course in summer before senior year: BME 188B and BME 188C. Note: students are expected to work on the iGEM project full-time in summer before senior year in preparation for the iGEM Grand Jamboree in October.

More information on BME research:

All BME 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, vaccine development, stem cell engineering, nano-electronic implants, assistive technologies, bioinformatics, microfluidics, nanoscale biotechnology, environmental monitoring, and other areas at the junction between engineering and the life sciences.

More information about BME research and undergraduate research opportunities can be found at Undergraduate Research Opportunities, the Genomics Institute, the Program in Biomedical Sciences and Engineering, and the STEM diversity programs.

Biomolecular engineering and bioinformatics students may continue their research and studies at UCSC in BME or a variety of graduate programs including biology, chemistry, biochemistry, and engineering programs such as computer science and engineering. 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 Expand and Collapse

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 Expand and Collapse

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
[e-mail]
[phone]

Getting Started in the Major: Frosh Expand and Collapse

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 Expand and Collapse

Transfer Admission Screening Policy Expand and Collapse

Transfer students need to complete the equivalent of eight courses from the following list with a GPA in those courses of 2.8 or better. Transfer students are not required to take additional coursework at UCSC to declare. This applies to all transfer students who complete eight courses, even if they didn't reach the 45 credits required to declare.

We calculate GPA from the eight courses from the list below using the UCSC grade points guidelines. If students take more than eight courses, all courses taken that apply toward transfer admissions screening requirements will be counted toward the GPA. For transfer courses from community colleges that do not include “+” or “-” we use the following: A=4.0, B=3.0, C=2.0, D=1.0.

BME 80G /PHIL 80G	Bioethics in the 21st Century: Science, Business, and Society	5
BIOL 20A	Cell and Molecular Biology	5
MATH 19A	Calculus for Science, Engineering, and Mathematics	5
MATH 19B	Calculus for Science, Engineering, and Mathematics	5
CHEM 8A	Organic Chemistry	5
CHEM 8B	Organic Chemistry	5
	Either one of these courses
AM 10	Linear Algebra for Engineers	5
MATH 21	Linear Algebra	5
	Either these courses
CHEM 3A	General Chemistry	5
CHEM 3B	General Chemistry	3
CHEM 3C	General Chemistry	3
	or these courses
CHEM 4A	Advanced General Chemistry: Molecular Structure and Reactivity	5
CHEM 4B	Advanced General Chemistry: Molecular Structure and Reactivity	5

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:

PHYS 5A	Introduction to Physics I	5
PHYS 5B	Introduction to Physics II	5
BME 21L	Introduction to Basic Laboratory Techniques	3

Transferring to Bioinformatics

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

CSE 16	Applied Discrete Mathematics	5
CSE 30	Programming Abstractions: Python	7

Transfer students may use courses articulated to PHIL 22, PHIL 24, or PHIL 28 in place of BME 80G, if these courses are taken prior to registering at UC Santa Cruz.

Getting Started in the Major: Transfer Students Expand and Collapse

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 Expand and Collapse

Major Qualification Expand and Collapse

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 Expand and Collapse

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 [phone] or email [e-mail].

How to Declare a Major Expand and Collapse

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

Letter Grade Policy Expand and Collapse

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

Course Substitution Policy Expand and Collapse

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 Expand and Collapse

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 Expand and Collapse

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 Expand and Collapse

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

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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. Due to course overlap, the biomolecular engineering and bioinformatics major (BMEB) B.S. cannot be combined with the biotechnology B.A. or the bioinformatics minor.

Course Requirements Expand and Collapse

Biomolecular engineering concentration majors must complete the following courses. Some courses may be satisfied via exam credit.

Lower-Division Courses Expand and Collapse

Biology

BIOL 20A

Cell and Molecular Biology

5

Bioethics

BME 80G /PHIL 80G

Bioethics in the 21st Century: Science, Business, and Society

5

General Chemistry

	Either these courses
CHEM 3A	General Chemistry	5
CHEM 3B	General Chemistry	3
CHEM 3BL	General Chemistry Lab	2
CHEM 3C	General Chemistry	3
CHEM 3CL	General Chemistry Lab	2
	or these courses
CHEM 4A	Advanced General Chemistry: Molecular Structure and Reactivity	5
CHEM 4AL	Advanced General Chemistry Lab	2
CHEM 4B	Advanced General Chemistry: Molecular Structure and Reactivity	5
CHEM 4BL	Advanced General Chemistry Lab	2

Note: This requirement may also be satisfied with prior completion of CHEM 1A, 1B, 1M, 1C, and 1N or equivalent.

Previous to July 1, 2023, the General Chemistry series, offered by the Department of Chemistry and Biochemistry, was listed in the General Catalog as CHEM 1A, CHEM 1B and CHEM 1C, with associated laboratories CHEM 1M and CHEM 1N. As of academic year 2023-24, this series was replaced with two distinct series: CHEM 3A, CHEM 3B and CHEM 3C, with labs CHEM 3BL and CHEM 3CL; or CHEM 4A and CHEM 4B with labs CHEM 4AL and CHEM 4BL. Descriptions of these two series are given here.

Organic Chemistry

All of the following courses:

CHEM 8A	Organic Chemistry	5
CHEM 8B	Organic Chemistry	5

CHEM 8B is a prerequisite for BIOC 100A, BIOL 100, and CHEM 103.

Both CHEM 8A and CHEM 8B are required for all biomolecular concentration students.

Laboratory Training

All of the following courses:

BME 21L	Introduction to Basic Laboratory Techniques	3
BME 22L	Foundations of Design and Experimentation in Molecular Biology	2

Mathematics

One of the following options:

	Either these courses
MATH 19A	Calculus for Science, Engineering, and Mathematics	5
MATH 19B	Calculus for Science, Engineering, and Mathematics	5
	or these courses
MATH 20A	Honors Calculus	5
MATH 20B	Honors Calculus	5

Plus one of the following:

AM 10	Linear Algebra for Engineers	5
MATH 21	Linear Algebra	5

Physics

	Either one of these courses
PHYS 5A	Introduction to Physics I	5
PHYS 15A	Honors Introduction to Physics I	5
	AND
PHYS 5L	Introduction to Physics I Laboratory	1
PHYS 5B	Introduction to Physics II	5
PHYS 5M	Introduction to Physics II Laboratory	1

Upper-Division Courses Expand and Collapse

Biochemistry and Molecular Biology

Choose one of the following options:

	Either these courses
BIOC 100A	Biochemistry and Molecular Biology	5
BIOC 100B	Biochemistry and Molecular Biology	5
	or these courses
BME 101	Molecular Biology for Biomolecular Engineers	5
CHEM 103	Biochemistry	5
	or these courses
BME 101	Molecular Biology for Biomolecular Engineers	5
BIOL 100	Biochemistry	5

CHEM 8B is a prerequisite for BIOC 100A, BIOL 100, and CHEM 103.

BIOE 20B is a prerequisite for BIOL 100.

BIOC 100A and BIOC 100B are strongly preferred for students who plan to pursue research in protein engineering, genetics, molecular biology, or biochemistry-related fields.

Biomolecular Engineering

Choose one of the following courses:

BME 105	Genetics in the Genomics Era	5
BIOL 105	Genetics	5

BME 105 is strongly recommended.

Plus all of the following courses:

BME 110	Computational Biology Tools	5
BME 160	Research Programming in the Life Sciences	6
BME 163	Applied Visualization and Analysis of Scientific Data	5

Plus one of the following Modeling/Design sequences:

	Either these courses
BME 128	Protein Engineering	5
BME 128L	Protein Engineering Laboratory	2
	or these courses
BME 177	Engineering Stem Cells	5
BME 177L	Engineering Stem Cell Laboratory	2
	or these courses
BME 130	Genomes	5
BME 123L	Long Read Sequencing	2

Statistics

STAT 131

Introduction to Probability Theory

5

Technical Writing

BME 185

Technical Writing for Biomolecular Engineers

5

This also satisfies the Disciplinary Communication (DC) requirement.

Elective Expand and Collapse

One of the following:

AM 115	Stochastic Modeling in Biology	5
METX 100	Introduction to Microbiology	5
METX 140	Molecular Biology and Microbial Genetics	5
BIOC 100C	Biochemistry and Molecular Biology	5
BIOL 115	Eukaryotic Molecular Biology	5
BME 118	Mathematics of the Mind	5
BME 122H	Extreme Environmental Virology	5
BME 123L	Long Read Sequencing	2
AM 147	Computational Methods and Applications	5
BME 128	Protein Engineering	5
BME 128L	Protein Engineering Laboratory	2
BME 130	Genomes	5
BME 132	Evolutionary Genomics	5
BME 140	Bioinstrumentation	5
BME 175	Entrepreneurship in Biotechnology	5
BME 177	Engineering Stem Cells	5
BME 177L	Engineering Stem Cell Laboratory	2
BME 178	Stem Cell Biology	5
ECE 104	Bioelectronics	5
	or any 5-credit biomolecular engineering graduate course

Graduate courses must be numbered BME 201-279.

This course cannot satisfy other requirements of the major.

Disciplinary Communication (DC) Requirement Expand and Collapse

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 the following course:

BME 185

Technical Writing for Biomolecular Engineers

5

Comprehensive Requirement Expand and Collapse

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 concentration students must complete one of the following options:

Option 1: BME Team Design

BME 129A	Project Design and Implementation in Biomolecular Engineering I	5
BME 129B	Project Design and Implementation in Biomolecular Engineering II	5
BME 129C	Project Design and Implementation in Biomolecular Engineering III	5

Option 2: iGEM

BME 180	Professional Practice in Bioengineering	2
BME 188A	Synthetic Biology--Mentored Research A	2
BME 188B	Synthetic Biology--Mentored Research B	5
BME 188C	Synthetic Biology Mentored Research C	5

Permission code required for enrollment in BME 188A, BME 188B, and BME 188C. Only students who have interviewed and been selected for the iGEM team in fall of their junior year may register for these courses.

Option 3: Bioinformatics Capstone

BME 205	Bioinformatics Models and Algorithms	5
BME 230A	Introduction to Computational Genomics and Systems Biology	5
BME 129C	Project Design and Implementation in Biomolecular Engineering III	5

Option 4: Senior Thesis

The thesis option consists of three quarters of BME 195, where students conduct research in biomolecular engineering or related field such as chemistry, biology, or biochemistry. 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 first quarter of BME 195. Students typically complete 15 credits of BME 195 during their senior year as follows: 5 credits per quarter fall/winter/spring.

BME 195

Senior Thesis Research

5

Permission code required for enrollment in BME 195. Permission code will be provided after student submits proposal (prior to first quarter of BME 195) or progress report (prior to second and third quarters of BME 195).

Exit Requirements Expand and Collapse

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 Expand and Collapse

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

Year	Fall	Winter	Spring	Summer
Entering				College 1A
				Summer Edge (optional)
1st (frosh)	MATH 19A	MATH 19B	AM 10
	CHEM 3A	CHEM 3B & CHEM 3BL	CHEM 3C & CHEM 3CL
		WRIT 1/WRIT 1E (if needed)
2nd (soph)	BME 21L	BME 22L	BME 105
	BIOL 20A	PHYS 5A & PHYS 5L	PHYS 5B & PHYS 5M
	CHEM 8A	CHEM 8B	STAT 131
	WRIT 2*
3rd (junior)	BIOC 100A	BIOC 100B	BME 163
	BME 110	BME 160	BME 177**
	BME 185		BME 177L**
4th (senior)	BME 129A	BME 129B	BME 129C
		Elective	BME 80G

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

** BME 177, BME 177L is one option for modeling/design sequence. Other options are offered in other quarters.

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	Summer
Entering				College 1A
				Summer Edge (optional)
1st (frosh)	CHEM 3A	MATH 19B	BIOL 20A	CHEM 8A
	MATH 19A	CHEM 3B & CHEM 3BL	CHEM 3C & CHEM 3CL	CHEM 8B
		WRIT 1/WRIT 1E (if needed)
2nd (soph)	BME 21L	BME 22L	BME 105
	BIOC 100A	BIOC 100B	BME 80G
	WRIT 2*	PHYS 5A & PHYS 5L	PHYS 5B & PHYS 5M
3rd (junior)	BME 110	BME 160	BME 163
	AM 10	BME 128**	BME 185
		BME 128L**
4th (senior)	BME 129A	BME 129B	BME 129C
	STAT 131		Elective

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

** BME 128, BME 128L is one option for modeling/design sequence. Other options are offered in other quarters.

General education requirements:

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

IM, 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.

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 course.

Transfer planner

Year	Fall	Winter	Spring	Summer
Entering				KRSG 1T
				Summer Edge (optional)
1st (junior)	BIOC 100A	BIOC 100B	BME 105
	BME 110	BME 160	BME 80G
	BME 185	BME 22L	BME 163
	BME 21L
2nd(senior)	BME 129A	BME 129B	BME 129C
	BME 130**	STAT 131	PHYS 5B & PHYS 5M
	BME 123L**	Elective

** BME 130, BME 123L is one option for modeling/design sequence. Other options are offered in other quarters.

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

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The bioinformatics concentration focuses on dry-lab (computational) techniques. Due to course overlap, the biomolecular engineering and bioinformatics major (BMEB) B.S. cannot be combined with the biotechnology B.A. or the bioinformatics minor.

Course Requirements Expand and Collapse

Bioinformatics concentration majors must complete the following courses. Some courses may be satisfied via exam credit.

Lower-Division Courses Expand and Collapse

Biology

BIOL 20A

Cell and Molecular Biology

5

Bioethics

BME 80G /PHIL 80G

Bioethics in the 21st Century: Science, Business, and Society

5

General Chemistry

	Either these courses
CHEM 3A	General Chemistry	5
CHEM 3B	General Chemistry	3
CHEM 3C	General Chemistry	3
CHEM 3BL	General Chemistry Lab	2
CHEM 3CL	General Chemistry Lab	2
	or these courses
CHEM 4A	Advanced General Chemistry: Molecular Structure and Reactivity	5
CHEM 4B	Advanced General Chemistry: Molecular Structure and Reactivity	5
CHEM 4AL	Advanced General Chemistry Lab	2
CHEM 4BL	Advanced General Chemistry Lab	2

Note: This requirement may also be satisfied with prior completion of CHEM 1A, 1B, 1M, 1C, and 1N or equivalent.

Previous to July 1, 2023, the General Chemistry series, offered by the Department of Chemistry and Biochemistry, was listed in the General Catalog as CHEM 1A, CHEM 1B and CHEM 1C, with associated laboratories CHEM 1M and CHEM 1N. As of academic year 2023-24, this series was replaced with two distinct series: CHEM 3A, CHEM 3B and CHEM 3C, with labs CHEM 3BL and CHEM 3CL; or CHEM 4A and CHEM 4B with labs CHEM 4AL and CHEM 4BL. Descriptions of these two series are given here.

Organic Chemistry

CHEM 8A

Organic Chemistry

5

Computer Science and Engineering

All of the following courses:

CSE 16	Applied Discrete Mathematics	5
CSE 30	Programming Abstractions: Python	7

Mathematics

One of the following options:

	Either these courses
MATH 19A	Calculus for Science, Engineering, and Mathematics	5
	or these courses
MATH 20A	Honors Calculus	5
MATH 20B	Honors Calculus	5

Plus one of the following:

AM 10	Linear Algebra for Engineers	5
MATH 21	Linear Algebra	5

Plus one of the following:

AM 30	Multivariate Calculus for Engineers	5
MATH 23A	Vector Calculus	5

Statistics

One of the following:

CSE 40	Machine Learning Basics: Data Analysis and Empirical Methods	5
STAT 132	Classical and Bayesian Inference	5

CSE 40 has a test-out option which can satisfy this requirement.

Upper-Division Courses Expand and Collapse

Data Structures and Algorithms

One of the following courses:

CSE 101	Introduction to Data Structures and Algorithms	5
CSE 101P	Introduction to Data Structures and Algorithms in Python	5

CSE 101 has an additional prerequisite of CSE 13S.

Biochemistry and Molecular Biology

One of the following courses:

BIOC 100A	Biochemistry and Molecular Biology	5
BIOL 100	Biochemistry	5
BME 101	Molecular Biology for Biomolecular Engineers	5
CHEM 103	Biochemistry	5

CHEM 8B is a prerequisite for BIOC 100A, BIOL 100, and CHEM 103.

BIOE 20B is a prerequisite for BIOL 100.

BME 101 is preferred.

Biomolecular Engineering

One of the following courses:

BME 105	Genetics in the Genomics Era	5
BIOL 105	Genetics	5

BME 105 is strongly recommended.

Plus all of the following courses:

BME 110	Computational Biology Tools	5
BME 160	Research Programming in the Life Sciences	6
BME 163	Applied Visualization and Analysis of Scientific Data	5

Bioinformatics concentration students may substitute CSE 20 for BME 160, although BME 160 is strongly recommended. CSE 20 has a test-out exam that will also be accepted. (Note: This substitution is not allowed for biomolecular concentration students.)

Statistics

STAT 131

Introduction to Probability Theory

5

Modeling and Design

One of the following:

CSE 142	Machine Learning	5
CSE 144	Applied Machine Learning: Deep Learning	5

Technical Writing

BME 185

Technical Writing for Biomolecular Engineers

5

Also satisfies the Disciplinary Communication (DC) requirement.

Elective Expand and Collapse

One of the following:

AM 115	Stochastic Modeling in Biology	5
AM 147	Computational Methods and Applications	5
BME 118	Mathematics of the Mind	5
BME 122H	Extreme Environmental Virology	5
BME 123L	Long Read Sequencing	2
BME 128	Protein Engineering	5
BME 128L	Protein Engineering Laboratory	2
BME 130	Genomes	5
BME 132	Evolutionary Genomics	5
BME 140	Bioinstrumentation	5
BME 175	Entrepreneurship in Biotechnology	5
BME 177	Engineering Stem Cells	5
BME 177L	Engineering Stem Cell Laboratory	2
BME 178	Stem Cell Biology	5
BIOC 100B	Biochemistry and Molecular Biology	5
CSE 142	Machine Learning	5
CSE 144	Applied Machine Learning: Deep Learning	5
CSE 182	Introduction to Database Management Systems	5
METX 100	Introduction to Microbiology	5
METX 140	Molecular Biology and Microbial Genetics	5
	or any 5-credit biomolecular engineering graduate course

Graduate courses must be numbered BME 201-279.

Courses satisfying an elective cannot be used to satisfy other requirements of the major.

Disciplinary Communication (DC) Requirement Expand and Collapse

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

BME 185

Technical Writing for Biomolecular Engineers

5

Comprehensive Requirement Expand and Collapse

All bioinformatics concentration students must complete a senior capstone project through one of the following options.

Note that the Technical Writing requirement BME 185 is a prerequisite for all capstone options. Students are responsible for ensuring that they meet the prerequisites for whichever capstone they choose.

Option 1: Bioinformatics Capstone

BME 205	Bioinformatics Models and Algorithms	5
BME 230A	Introduction to Computational Genomics and Systems Biology	5
BME 129C	Project Design and Implementation in Biomolecular Engineering III	5

Option 2: Senior Thesis

The thesis option consists of three quarters of BME 195, where students conduct research in biomolecular engineering or related field such as chemistry, biology, or biochemistry. 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 first quarter of BME 195. Students typically complete 15 credits of BME 195 during their senior year as follows: 5 credits per quarter fall/winter/spring.

BME 195

Senior Thesis Research

5

Permission code required for enrollment in BME 195. Permission code will be provided after student submits proposal (prior to first quarter of BME 195) or progress report (prior to second and third quarters of BME 195).

Exit Requirements Expand and Collapse

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 Expand and Collapse

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

Year	Fall	Winter	Spring		Summer
Entering					College 1A
					Summer Edge (optional)
1st (frosh)	CHEM 3A	CHEM 3B & CHEM 3BL	CHEM 3C & CHEM 3CL
	MATH 19A	MATH 19B	BIOL 20A
	College 1	WRIT 1/WRIT 1E (if needed)
2nd (soph)	CHEM 8A	CHEM 8B	BME 105
	AM 10	CSE 16	BME 80G
	WRIT 2*	BME 160	AM 30
3rd (junior)	BME 110	BME 101	BME 163
	STAT 131	STAT 132	BME 185
	CSE 30		CSE 101P
4th (senior)	BME 205	BME 230A	BME 129C
	Elective		CSE 142 or CSE 144

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

General education requirements:

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

IM, 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 course.

Transfer planner

Year	Fall	Winter	Spring	Summer
Entering				KRSG 1T
				Summer Edge (optional)
3rd (junior)	AM 10	BME 101	BME 105
	STAT 131	BME 160	BME 163
	AM 30	STAT 132	CSE 101P
4th (senior)	BME 205	BME 230A	BME 129C
	BME 110	CSE 142 or CSE 144	BME 80G
	BME 185	Elective

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.