Biomolecular Engineering

The program in bioinformatics is a multidisciplinary program involving faculty of the Center for Biomolecular Science and Engineering. The program offers B.S., M.S., and Ph.D. degrees in 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. 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 UC Santa Cruz in 1985. One notable output from our research is that UCSC is the primary release site for the public version of the human genome and its annotation: http://genome.ucsc.edu. We are also a major player in protein-structure prediction.

The undergraduate bioinformatics degree program prepares students for graduate school or a career in the fast-paced 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 mathematics, 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 a bioinformatics course, Biomolecular Engineering 100/L, Introduction to Bioinformatics/Laboratory. Students have two electives for specialization within the field of bioinformatics and are required to take a bioethics course, course 80G, Bioethics in the Twenty-First Century: Science, Business, and Society, to study the ethical, legal, and social implications of this new technology. As a comprehensive requirement, all students complete a graduate project course: Biomolecular Engineering 220/L (formerly Computer Science 243), Protein Bioinformatics/ Laboratory, or Biomolecular Engineering 230/L, (formerly Computer Science 244), Computational Genomics/ Laboratory.

Note: students who work on independent research projects with faculty may substitute a senior thesis, Biomolecular Engineering 195, for the graduate project course.

Courses for Nonmajors

Biomolecular Engineering 60, Programming for Biologists and Biochemists, provides 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 Engineering 110, 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 100/L, Introduction to Bioinformatics/Laboratory, provides a detailed look at some of the important algorithms and theory that is used in bioinformatics tools. It may be of interest to majors in chemistry, biology, computer science, and mathematics.

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.

Bioinformatics Policies

Admissions Policy

Admission to the bioinformatics major is selective. First-year applicants may receive direct admission at the time they apply to UC Santa Cruz, 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 the foundation courses: Computer Science 13H (or 12A and 12B), Chemistry 1B/M and 1C/N, and Mathematics 19A-B. Please refer to the School of Engineering section of the catalog for the full admissions policy.

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 UC Santa Cruz.

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.

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.

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

21A, Accelerated Cell and Molecular Biology; or
20A, Cell and Molecular Biology
21B, Accelerated Development and Physiology; or
20B, Development and Physiology

Biomolecular Engineering

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

Chemistry

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

Computer Engineering

16H, Honors Applied Discrete Mathematics; or
16, Applied Discrete Mathematics

Computer Science

13H/L, Introduction to Programming and Data Structures (Honors)/Laboratory; or both 12A/L, Introduction to Programming/Laboratory and 12B/M, Introduction to Data Structures

Mathematics

20A and 20B, 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:

Biochemistry and Molecular Biology

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

Bioinformatics

Biomolecular Engineering 100/L, Introduction to Bioinformatics/Laboratory
Biomolecular Engineering 110, Computational Biology Tools
One of the following:
Biomolecular Engineering 220/L, Protein Bioinformatics/Laboratory; or 230/L, Computational Genomics/Laboratory; or 195, Senior Thesis Research

Chemistry

108A/L, Organic Chemistry/Laboratory; or
112A/L, 112B/M, Organic Chemistry/Laboratory (two-thirds of three-part sequence)

Probability and Statistics

Computer Engineering 107, Mathematical Methods of Systems Analysis: Stochastic; or Applied Mathematics and Statistics 131, Introduction to Probability Theory (formerly Mathematics 131A); and 206, Bayesian Statistics

Computer Engineering

185, Technical Writing; or W section of Biology 20L, Experimental Biology Laboratory

Computer Science

101, Abstract Data Types
180, Database Systems

Advanced Programming

One of the following five courses:
Computer Engineering 177, Applied Graph Theory and Algorithms; or Computer Science 104A, Fundamentals of Compiler Design I; or Computer Science 109, Advanced Programming; or Computer Science 115, Software Methodology; or Biomolecular Engineering 109, Resource-Efficient Programming

Required Electives
With preapproval from the undergraduate director for bioinformatics, students must select two additional courses as electives. The following courses are typical of the ones chosen:

Biochemistry 100B, 100C, 110
Biology 102L, 105 or 106, 105L, 109L, 110, 115, 116L, 117A, 187L, 210
Biomolecular Engineering 109, 110, 220/L, 230/L
Chemistry 108B/M
Computer Engineering 108, 150, 151, 177
Computer Science 104A, 104B, 109, 115, 116, 130, 160
Applied Mathematics and Statistics 147, 162, 203, 205

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

Comprehensive Requirement

The bioinformatics comprehensive requirement can be met by taking Biomolecular Engineering 220/L, Protein Bioinformatics/Laboratory, or Biomolecular Engineering 230/L, Computational Genomics/Laboratory, which includes 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 prior to submitting the final thesis.

Bioinformatics Major Planners

Plan One is a suggested plan for students who are undecided between bioinformatics and another School of Engineering major. Plan Two is suggested for students undecided between bioinformatics and some other field in biology or chemistry. Four-year plans require individual design to fit in the desired electives, so only the first two years of the academic plans are presented here.

The Bioinformatics Minor

The bioinformatics minor consists of the following 16 courses:

Lower-Division Requirements (11 courses)

. Biology (two courses): Biology 20A and 20B or 21A and 21B

. General chemistry (two courses): Chemistry 1B/M and 1C/N

. Calculus (three courses): Mathematics 19A-B and 23A; or Mathematics 11A-B and 22; or Mathematics 20A and 20B and 23A.

. Discrete math (one course): Computer Engineering 16 or 16H

. Programming (two courses): Computer Science 12A/L and 12B/M; or Computer Science 13H/L

. Bioethics (one course): Biomolecular Engineering 80G or Philosophy 145

Upper-Division Requirements (five courses)

. Organic chemistry (one course): Chemistry 108A; or Chemistry 112A-B

. Biochemistry (one course): Biochemistry and Molecular Biology 100A or Biology 100

. Statistics (one course): Computer Engineering 107 or Applied Mathematics and Statistics 131

. Programming (one course): Computer Science 101 or Biomolecular Engineering 109

. Bioinformatics (one course): Bioinformatics 100/L or 110

A bioinformatics minor may apply the upper-division courses in organic chemistry (Chemistry 108 or 112A-B), biochemistry (Biochemistry 100A or Biology 100), statistics (Computer Engineering 107 or Applied Mathematics and Statistics 131), and programming (Computer Science 101 or Biomolecular Engineering 101) to both the minor and another major or minor. If Biomolecular Engineering 100/L are applied to another degree, they must be replaced by an appropriate bioinformatics elective approved by the program. Majors with substantial overlap with bioinformatics include biochemistry; chemistry; computer science; computer engineering; and molecular, cell, and developmental biology. For example, a biochemistry and molecular biology major, chemistry major with biochemistry emphasis, or MCD biology major could double-count the biology, general chemistry, calculus, organic chemistry, and biochemistry courses. A chemistry major could double-count general chemistry, calculus, organic chemistry, computer science 12A, and biochemistry courses. A computer science major could double-count the programming, discrete math, calculus, and statistics classes. A computer engineering major could double-count the bioethics, chemistry, programming, discrete math, calculus, and statistics classes.

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./M.S. and B.S./Ph.D. program that allows our B.S. students to complete the M.S. (or Ph.D.) somewhat sooner than master's students with less tailored preparation.

The current B.S. and graduate requirements have four courses in common:

. Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society; or Philosophy 145/245, Brave New World: Ethical Issues in Genetics

. Biomolecular Engineering 100/L, Introduction to Bioinformatics/Laboratory

. Biomolecular Engineering 220/L, Protein Bioinformatics/Laboratory; or 230/L, Computational Genomics/Laboratory

. Applied Mathematics and Statistics 206, Bayesian Statistics

Master's students normally take nine courses plus two seminars (4 credits) and Biomolecular Engineering 200. The course work for Ph.D. students is the same, except that 8 credits of seminars are required.

The combined B.S./graduate program does not make any changes to the undergraduate program, except that students must pass the four overlapping courses listed above with 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 courses required is reduced from nine to seven, plus the seminar requirements.

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 will automatically be included in the combined B.S./M.S. or B.S./Ph.D. program.

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.

Core courses (5 credit)-seven are required
Biomolecular Engineering

. 100/L, Introduction to Bioinformatics/Laboratory

. 220/L, Protein Bioinformatics/Laboratory

. 230/L, Computational Genomics/Laboratory

. 80G, Bioethics in the Twenty-First Century: Science, Business, and Society; or Philosophy 245, Brave New World: Ethical Issues in Genetics

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 200A 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 (formerly Computer Engineering 280B)

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

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 should be submitted to a faculty member by the end of the third 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 and must be accepted by 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 select a faculty research adviser by the end of the second year. A written dissertation proposal will be submitted to the adviser. 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 his or her 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.

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.