Biomolecular Engineering

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

Program Description

The Department of Biomolecular Engineering is an interdisciplinary department that combines expertise from Biology, Mathematics, Chemistry, Computer Science, and Engineering to train students and develop technologies to address major problems at the forefront of biomedical and bio-industrial research.  Students trained in the Department of Biomolecular Engineering can look forward to careers in Academia, the Information and Biotechnology Industries, Public Health, or Medical Sciences. 

The department currently offers an undergraduate minor, B.S, M.S., and Ph.D. degrees in bioinformatics.  The department co-sponsors the B.S. in Bioengineering program, described elsewhere in this catalog, with the Departments of Computer Engineering, Electrical Engineering, and Molecular, Cell, and Developmental (MCD) Biology. 

Departmental faculty advise undergraduate and graduate researchers enrolled in the bioinformatics, bioengineering, and related degree programs.  Members of the BME Department actively collaborate with faculty from other Baskin School of Engineering departments, such as Applied Mathematics & Statistics, Computer Engineering, Computer Science, and Electrical Engineering; and with the Physical & Biological Sciences departments of MCD Biology, Chemistry and Biochemistry, Microbiology and Environmental Toxicology, Ecology and Evolutionary Biology, and Ocean Sciences.

Bioinformatics

Bioinformatics 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 Center for Biomolecular Science and Engineering, http://cbse.ucsc.edu.

The Human Genome Project, the international collaboration to determine the sequence of human DNA and understand its function, had its origin in a conference that took place at UCSC in 1985.  One notable output from our research is that UCSC is the primary release site for the public version of the human genome: http://genome.ucsc.edu, as well as the repository for the ENCODE project, a national effort to annotate the entire human genome with multiple functional assays.  We are also a major player in protein-structure prediction, and have a strong research group in DNA microarray analysis.

The undergraduate bioinformatics degree program prepares students for graduate school or a career in the pharmaceutical or biotechnology industries.

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 program 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.

The undergraduate degree program in bioinformatics builds a solid foundation in the constituent areas of the field. Students complete core sequences in mathematics (including calculus, statistics, and discrete mathematics), science (including biology, chemistry, and biochemistry), and engineering (including programming, algorithms, and databases). The core topics are brought together in two bioinformatics courses: BME 110, Computational Biology Tools, and BME 205, Bioinformatics Models and Algorithms. Students have two electives for specialization within the fields of bioinformatics and are required to take a bioethics course (either BME 80G, Bioethics in the Twenty-First Century: Science, Business, and Society or PHIL 145, Brave New World: Ethical Issues in Genetics) to study the ethical, legal, and social implications of this new technology. As a comprehensive requirement, all students complete a graduate project course: BME 210, Experimental Systems Biology, BME 211, Computational Systems Biology, BME 220/L, Protein Bioinformatics, or BME 230/L, Computational Genomics. Students who work on independent research projects with faculty (as all students are encouraged to do) may substitute a senior thesis, BME 195, for the graduate project course.

Courses for Nonmajors

Biomolecular Engineering 5, Introduction to Biotechnology, presents a broad overview of the impact of biotechnology on the diagnosis and treatment of disease.

Biomolecular Engineering 60 and 160, Programming for Biologists and Biochemists, provide an introductory programming class using Perl and BioPerl to analyze, transform, and publish biological data.

Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society, is particularly appropriate to all students interested in the societal issues surrounding the revolutions in bioinformatics and biotechnology. 

Biomolecular Engineering110, Computational Biology Tools, provides an introduction to the tools and techniques of bioinformatics from a user’s view. It is intended for biologists and biochemists who need to use bioinformatics tools, but are not primarily interested in building new bioinformatics tools.

Biomolecular Engineering 109, Resource-efficient Programming, provides advice and practice for people working at the limits of their computer hardware.  It is of use for bioinformaticians, game programmers, and embedded-system designers.

Biomolecular Engineering 155, Biotechnology and Drug Development, examines the science and process of discovering, testing, and manufacturing new drugs within the pharmaceutical industry. 

Bioinformatics Policies

Admissions Policy

Admission to the bioinformatics major is selective. First-year applicants may receive direct admission at the time they apply to UCSC, based on their high school record and test scores.
Admission to the bioinformatics major after a student has entered UCSC is based on performance in courses offered by the School of Engineering and the Division of Physical and Biological Sciences (the SOE GPA). Due to the required graduate courses in the senior years, a School of Engineering GPA of 2.9 or better is expected at the time of major declaration. After the first year, the following foundation courses must be completed before admission to the major: Computer Science 12A/L (or 5J and 11 or Computer Engineering 12/L and 13/L) and Computer Science 12B, Chemistry 1A, 1B/M and 1C/N, and Mathematics 19A-B.

Courses Taken Elsewhere

Please refer to the School of Engineering section of the catalog for policies about taking courses at other institutions after enrolling at UCSC.

Disqualification Policy

Students who do not make adequate progress in the major (normally passing six required courses per year) may be disqualified from the major. All students not meeting the progress in the major or grade point average requirements must meet with the undergraduate director to discuss their options for continuing in the major. Please refer to the Engineering section of this catalog for the School of Engineering’s Major Disqualification Policy.

Honors in the Major

Bioinformatics majors are considered for “Honors in the Major” and “Highest Honors in the Major” based on the School of Engineering GPA and on results of undergraduate research. Students with an SOE GPA of 3.7 in most cases receive Highest Honors. Students with an SOE GPA of 3.3 in most cases receive Honors. Students with particularly significant accomplishments in undergraduate research may be considered with a lower SOE GPA.

Transfer Students

Please refer to the School of Engineering section of the catalog for the policy regarding transfer students.

School of Engineering Policies

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

Preparation for the Major

Students applying for admission to the 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.

Bioinformatics Major Requirements

Every 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 course work that meets the major requirements. Because of the enormous breadth of requirements, 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.

Lower-Division Requirements

Majors must complete the following lower-division courses:

Biology

20A, Cell and Molecular Biology 

Biomolecular Engineering

80G, Bioethics in the Twenty-First Century: Science, Business, and Society; or
Philosophy 145, Brave New World: Ethical Issues in Genetics

Chemistry

1A, 1B/M, and 1C/N, General Chemistry/Laboratory

Computer Engineering

16, Applied Discrete Mathematics

Programming 1

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 13/L, Computer Systems and C Programming/Laboratory

Programming 2

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

Mathematics
20A-B, Honors Calculus; or
19A-B, Calculus for Science, Engineering, and Mathematics (Credit for one or both can be granted with adequate performance on the CEEB calculus AB or BC Advanced Placement examination.)
23A, Multivariable Calculus

Upper-Division Requirements

Majors must complete the following upper-division courses:

Applied Mathematics and Statistics

Computer Engineering 107, Mathematical Methods of Systems Analysis: Stochastic; or
Applied Mathematics andStatistics 131, Introduction to Probability Theory
Applied Mathematics and Statistics 206, Bayesian Statistics; or
Applied Mathematics and Statistics 132, Statistical Inference

Biochemistry and Molecular Biology

100A, Biochemistry (first in three-part sequence)

Bioinformatics

Biomolecular Engineering 110, Computational Biology Tools
Biomolecular Engineering 205, Bioinformatics Models and Algorithms

One of the following:
Biomolecular Engineering 210, Experimental Systems Biology; or
Biomolecular Engineering 211, Computational Systems Biology; or
Biomolecular Engineering 220/L, Protein Bioinformatics/Laboratory; or 
Biomolecular Engineering 230/L, Computational Genomics/Laboratory; or 
Biomolecular Engineering 195, Senior Thesis Research

Biology

Biology 105, Genetics

One of the following:
Biology 110, Cell Biology; or
Biology 115, Eukaryotic Molecular Biology; or
Biology 119, Microbiology; or
Biomolecular Engineering 155, Biotechnology and Drug Development

Chemistry

108A/L, Organic Chemistry/Laboratory; or
112A/L and 112B/M, Organic Chemistry/Laboratory

Computer Engineering

185, Technical Writing for Computer Engineers

Computer Science

One of the following:
182, Introduction to Database Management Systems, or
180, Database Systems.  Note that CMPS 180 may require an additional course as a prerequisite, such as CMPS 101.

Advanced Programming

Computer Science 109, Advanced Programming

Required Electives

Students must select two additional courses as electives, justify their choices in writing, and get the choices approved by their faculty adviser. The following courses are typical of the ones chosen, but do not constitute a pre-approved list:

Applied Mathematics and Statistics 132, 162, 203, 205, 207, 215
Biochemistry 100B, 100C, 110
Biology 100L, 105L, 105M, 109L, 110, 115, 115L, 117A, 117B, 119, 119L, 187L, 200A, 200B
Biomolecular Engineering 102, 109, 130, 210, 220, 230
Chemistry 103, 108B/M, 112C/N, 200A, 200B, 200C
Computer Engineering 108, 177
Computer Science 101, 104A, 105,  115, 116, 130, 140, 142, 160/L
Information Systems Management 206, 250

Note: many of these courses are offered only once a year and have long prerequisite chains, so advance planning is necessary to make sure elective courses can be fit into the student’s schedule. 

Disciplinary Communication (DC) Requirement

Students of every major must satisfy that major's upper-division Disciplinary Communication (DC) requirement. The DC requirement will normally be met within one to three courses already required for the major. For detailed information on this major’s DC requirement, consult your major adviser or see the 2010-11 general catalog.

Comprehensive Requirement

The bioinformatics comprehensive requirement can be met by taking Biomolecular Engineering 210, Experimental Systems Biology, or Biomolecular Engineering 211, Computational Systems Biology, or Biomolecular Engineering 220/L, Protein Bioinformatics, or Biomolecular Engineering 230/L, Computational Genomics, which include substantial projects; or Biomolecular Engineering 195, Senior Thesis Research. Students electing the senior thesis must submit a written thesis proposal to the undergraduate director of bioinformatics for approval one quarter prior to submitting the final thesis.

The Bioinformatics Minor

Where the bioinformatics major is intended for people who wish to become bioinformaticians and create the tools needed to solve new problems in computational biology, the bioinformatics minor is intended primarily for bioinformatics tool users who are majoring in a biological or chemical specialty. The bioinformatics minor is also appropriate for computer science or computer engineering majors who are considering graduate work in bioinformatics.
A bioinformatics minor consists of the following 15 courses:

Lower-division (10 courses)

Biology (2)

20A, Cell and Molecular Biology; and

One of the following:
Biology 20B, Ecology and Evolutionary Biology; or
Biology 110, Cell Biology; or
Biology 105, Genetics; or
Biology 115, Eukaryotic Molecular Biology; or
Biology 119, Microbiology

General chemistry (3)

Chemistry 1A, Chemistry 1B/M and Chemistry 1C/N

Single-Variable Calculus (2)

Mathematics 19A and Mathematics 19B—preferred; or
Mathematics11A and Mathematics 11B; or
Mathematics 20A and Mathematics 20B

Programming 1 (1)

Computer Science 12A/L; or
Computer Science 5C; or
Computer Science 5J; or
Computer Science 5P; or
Computer Engineering 12/L and Computer Engineering 13/L

Programming 2 (1)

Biomolecular Engineering 160/L; or
Computer Science 12B/M

Bioethics (1)

Biomolecular Engineering 80G; or
Philosophy 145; or
Biomolecular Engineering 247

Upper-division (5 courses)

Organic chemistry (1)

Chemistry 108A; or
Chemistry 112A and CHEM 112B

Biochemistry (1)

Biochemistry 100A; or
Biology 100

Statistics (1)

Computer Engineering 107; or
Applied Mathematics and Statistics 131

Bioinformatics (1)

Biomolecular Engineering 110

Elective(1)

Applied Mathematics and Statistics 132; or
Biochemistry 100B; or
any other upper-division or graduate biomolecular
engineering course

The bioinformatics minor requirements may satisfy the requirements of other majors or minors under the campus policy discussed in Major and Minor Requirements. Majors with substantial overlap include biochemistry, bioengineering, all biology majors, chemistry, computer science, and computer engineering. Students pursing one of these majors are particularly encouraged to consider the bioinformatics minor.

The Bioinformatics Combined B.S./Graduate Degree Program

Because our bioinformatics B.S. program provides excellent preparation for a graduate program in bioinformatics, we offer a combined B.S./grad program that allows our B.S. students to complete the M.S. (or Ph.D.) somewhat sooner than students with a less tailored preparation.
The current B.S. and graduate requirements have four courses in common:

Biomolecular Engineering 80G, Bioethics in the 21st Century; or Philosophy 145/245, Brave New World: Ethical Issues in Genetics
Biomolecular Engineering 205, Bioinformatics Models and Algorithms
Biomolecular Engineering 220, Protein Bioinformatics; or Biomolecular Engineering 230, Computational Genomics
Applied Mathematics and Statistics 206, Bayesian Statistics

Masters students take nine courses, two seminars (four credits), Biomolecular Engineering 200, and two independent project courses (such as Biomolecular Engineering 220L and Biomolecular Engineering 230L). The course work for Ph.D. students is essentially the same, except that eight credits of seminars are required and three research lab rotations are required in place of the two project courses.

The combined B.S./graduate degree program does not make any changes to the undergraduate program, except that students must pass the four overlapping courses listed above for a grade of B- or better.

The requirements at the graduate level are changed to remove the four courses that overlap with the B.S. and to add two graduate electives to be chosen by the students with the approval of their advisers.  Thus, the total number of full courses required is reduced from nine to seven.
To apply for the combined program, students apply to the M.S. or Ph.D. program through the normal graduate admission process in the fall of their senior year.  If admitted into the graduate program, they would automatically be included in the combined B.S./M.S. or B.S./Ph.D. program.

Bioinformatics Major Planners

Plan one is a suggested plan for students who are undecided between bioinformatics and another computing major. Plan two is suggested for students undecided between bioinformatics and some other field in biology or chemistry.  As in all engineering and science programs, it is recommended that students spread their general education requirements out over all 12 quarters. Students considering pursuing a bioengineering degree should follow the biomolecular concentration of the bioengineering B.S. program and complete the programming sequence (Computer Science 12A and 12B) by the end of their second year.

Four-year plans require individual design to fit in the desired electives, so only the first two years of the academic plan are presented here.  It is recommended that students reserve the summer after the junior year for undergraduate research. One popular plan involves taking organic chemistry and the associated labs in the summer after completing general chemistry, so that biochemistry may be started in the junior year.

Most students find it easiest to take Biomolecular Engineering 205, Bioinformatics Models and Algorithms, after Biomolecular Engineering 110, Computational Biology Tools.

Year	Fall	Winter	Spring
1st (frsh)	MATH 19A CHEM 1A core	MATH 19B CHEM 1B/M gen ed	MATH 23A CHEM 1C/N gen ed
2nd (soph)	CMPE 16 CHEM 108 A/L BME 80G	CMPS 12A/L BIOL 20A gen ed	CMPS 12B/M BIOL 105 gen ed

Bioinformatics Graduate Program

The graduate program in bioinformatics offers both M.S. and Ph.D. degrees.

Course Requirements

Both masters and doctoral students must complete nine, 5-credit courses (seven core courses and two electives; see below) and a 3-credit research and teaching course. In addition, M.S. students must complete four seminar credits, while Ph.D. students must complete eight seminar credits. M.S. students must complete two (1-credit or 2-credit) research project courses (such as course 220L, 230L, 297F, or 297), and Ph.D. students must complete three research lab rotations (course 296) with different supervisors.

Core courses (5-credit)–seven are required

Biomolecular Engineering

205, Bioinformatics Models and Algorithms

Two other graduate bioinformatics courses (courses in the range 210-239)

80G, Bioethics in the Twenty-First Century: Science, Business, and Society; or Philosophy 245, Brave New World: Ethical Issues in Genetics; or 247, Stem Cell Research; Scientific, Ethical, Social and Legal Issues

One graduate course, approved by the faculty, in each of the following three areas:

Statistics (Applied Mathematics and Statistics 206 recommended)
Biology (Biology 200B recommended)
Chemistry (Chemistry 200B recommended)

Electives (5-credit)–two are required

The electives should be graduate-level courses selected with approval of the faculty to ensure a coherent, balanced program. For M.S. students, 5 credits of independent research (297) or thesis research (299) may count as electives toward the degree requirements upon approval of the faculty. For Ph.D. students, independent or thesis research cannot be counted as electives.
Students must choose their electives with faculty guidance and approval to balance their preparation and make up for deficiencies in background areas. In addition to fulfilling background needs, students may choose to emphasize one of the breadth areas: molecular biology, biochemistry, statistics, computational biology, genetics, computer science, computer engineering, applied mathematics, cell biology, and computer graphics/visualization or may take a cross-sampling of the electives to achieve a broad knowledge base.

Other Curriculum Requirements

Biomolecular Engineering 200, Research and Teaching in Bioinformatics, 3 credits

Seminars

M.S. students: a minimum of two seminar courses, including at least one quarter of the 2-credit Biomolecular Engineering seminar, 280B

Ph.D. students: a minimum of four seminar courses, including at least two quarters of the 2-credit Biomolecular Engineering Seminar, 280B

Research experience

M.S. students: a minimum of two research project courses. This requirement can be met by taking course 220L, 230L, and/or independent study (course 297F or course 297).

Ph.D. Students: three quarters of lab rotations (course 296), generally within the first 12 months. One of the lab rotations must be with a faculty supervisor who does wet-lab research, though the student’s rotation project may be purely computational.

Qualifying Exams

Ph.D. students are required to pass an oral qualifying exam by the end of their second year and to advance to candidacy by the end of their third year.

Adequate Progress

Graduate students receiving two or more U (unsatisfactory) grades or grades below B in courses relevant to the program are not making adequate progress and will be placed on academic probation for the next three quarters of registered enrollment.

Graduate students who fail (unsatisfactory or lower than B) a relevant course while on probation may be dismissed from the program. Students may appeal their dismissal. Graduate students who fail a relevant course after being removed from probation are immediately returned to academic probation.

Graduate students experiencing circumstances that may adversely affect their academic performance should consult with their adviser and the graduate director.

Thesis and Dissertation Requirements

In addition to completing the course requirements, students must fulfill the following thesis or dissertation requirements.

For M.S. students, a written thesis proposal must be submitted to a faculty member before the end of the fourth academic quarter. If the faculty member accepts the proposal, he or she will become the student’s adviser and will be in charge of supervising the writing of the master’s thesis. When the thesis is completed, it will be submitted to a faculty review committee consisting of the thesis adviser and at least two additional readers. The committee must include a School of Engineering faculty member, may include participants from the Division of Physical and Biological Sciences and from industry as appropriate, and must be approved by the bioinformatics program director. Students are required to present their thesis project in a public seminar.

Ph.D. students must pass an oral comprehensive exam by the end of the second year.

Ph.D. students must select a faculty research adviser by the end of the second year.  A qualifying committee is then formed, which consists of the adviser and three additional members, and approved by the bioinformatics program director and the campus graduate dean. The student must submit  a written dissertation proposal to all members of the committee and the graduate assistant one month in advance of the examination. The dissertation proposal is publicly and formally presented in an oral qualifying examination given by the qualifying committee. This exam must be completed within six months of a successful comprehensive exam.

Ph.D. candidates will submit the completed dissertation to a reading committee at least one month prior to the dissertation defense. The reading committee, formed upon advancement to candidacy, consists of the dissertation supervisor and two readers appointed by the program director upon the recommendation of the dissertation supervisor. The candidate will present his or her research in a public seminar. The seminar will be followed by a defense of the dissertation to the reading committee and attending faculty, who will then decide whether the dissertation is acceptable or requires revision.

Transfer Limitations
Up to two courses may be transferred from other graduate institutions, with the approval of the faculty adviser and the graduate director.