Biomolecular Engineering
2013-14 General Catalog
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 offers an undergraduate minor and a bachelor of science (B.S.) degree in bioinformatics, and graduate master of science (M.S.) and doctor of philosophy (Ph.D.) degrees in biomolecular engineering and 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. The department co-sponsors the Program in Biomedical Science and Engineering (PBSE), a doctoral training program, with the departments of MCD Biology, Chemistry and Biochemistry, and Microbiology and Environmental Toxicology.
Departmental faculty advise undergraduate and graduate researchers enrolled in the bioinformatics, bioengineering, and related degree programs. Members of the Department of Biomolecular Engineering actively collaborate with faculty from other Baskin School of Engineering departments, such as Applied Mathematics and Statistics, Computer Engineering, Computer Science, and Electrical Engineering; and with the Physical and Biological Sciences departments of MCD Biology, Chemistry and Biochemistry, Microbiology and Environmental Toxicology, Ecology and Evolutionary Biology, and Ocean Sciences.
Bioinformatics Major
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 (Encyclopedia Of DNA Elements) project, a national effort to annotate the entire human genome with multiple functional assays. We also have a strong research group in systems biology, functional genomic characterization of stem cells, and play a lead role in national efforts to discover molecular underpinnings of various cancers, including participating as a Dream Team for the Stand Up To Cancer project and a data-analysis center for The Cancer Genome Atlas project.
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: Biomolecular Engineering 110, Computational Biology Tools, and Biomolecular Engineering 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 Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society or Philosophy 145, Brave New World: Ethical Issues in Genetics) to study the ethical, legal, and social implications of this new technology.
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, provides an introductory programming class using Python and BioPython 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 users 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 130, Genomes Genome-scale analysis to answer biological questions.
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
Declaration of the Major
Admission to the bioinformatics major after a student has entered UCSC is based on grades received in all School of Engineering (SOE) and Division of Physical and Biological Sciences courses taken. Due to the required graduate courses in the senior years, a cumulative GPA of 2.90 or better in these courses is expected at the time of major declaration. Students are strongly advised not to request Pass/No Pass grading in any School of Engineering or Division of Physical and Biological Sciences courses since a grade of P will be treated as a C for calculating the GPA regardless of the content of the evaluation. No Pass grades are treated as an F. Although the campus GPA excludes the first 15 credits of repeated courses from the GPA calculation, all attempts are included in the GPA calculation described here. In addition to this GPA requirement, 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/M, Chemistry 1A, 1B/M and 1C/N, and Mathematics 19A-B.
Students who are informed that they are not eligible to declare the major may appeal this decision by submitting a letter to the department chair within 15 days from the date the notification was mailed. Within 15 days of receipt of the appeal, the department will notify the student, college, and Office of the Registrar of the decision.
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.
Honors in the Major
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, in most cases, receive "Highest Honors in the Major." Students with a GPA of 3.3, in most cases, receive "Honors in the Major." Students with particularly significant accomplishments in undergraduate research may be considered with a lower GPA.
Transfer Students
Transfer admission is based on math, programming, chemistry, and biology courses, which are among the most highly articulated courses in California.
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.
Requirements of the Bioinformatics Major
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
Biology (BIOL) 20A, Cell and Molecular Biology
Biomolecular Engineering
Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society; or
Philosophy 145, Brave New World: Ethical Issues in Genetics; or
BME 247, Stem Cell Ethics
Chemistry
Chemistry 1A, 1B/M, and 1C/N, General Chemistry/Laboratory
Computer Engineering
Computer Engineering 16, Applied Discrete Mathematics
Programming 1
Computer Science 12A/L, Introduction to Programming/Laboratory (accelerated); 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
Mathematics 20A-B, Honors Calculus; or
Mathematics 19A-B, Calculus for Science, Engineering, and Mathematics (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.)
Mathematics 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 and Statistics 131, Introduction to Probability Theory
Applied Mathematics and Statistics 206, Bayesian Statistics; or
Applied Mathematics and Statistics 132, Statistical Inference
Biochemistry and Molecular Biology
Biochemistry 100A, Biochemistry (first in three-part sequence); or
Biology 100K, Biochemistry Laboratory
Bioinformatics
Biomolecular Engineering 110, Computational Biology Tools
Biomolecular Engineering 205, Bioinformatics Models and Algorithms
One of the following:
Biomolecular Engineering 211, Computational Systems Biology; or
Biomolecular Engineering 230/L, Computational Genomics/Laboratory; or
Biomolecular Engineering 195, Senior Thesis Research
Biology (BIOL)
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
Chemistry 108A/L, Organic Chemistry/Laboratory; or
Chemistry 112A/L and 112B/M, Organic Chemistry/Laboratory
Computer Engineering
Computer Engineering 185, Technical Writing for Computer Engineers
Computer Science
Computer Science 101, Algorithms and Abstract Data Types
One of the following:
Computer Science 182, Introduction to Database Management Systems, or
Computer Science 180, Database Systems.
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, 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
Technology and Information 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. Bioinformatics majors satisfy the DC requirement by completing Computer Engineering 185, Technical Writing for Engineers.
Comprehensive Requirement
The bioinformatics comprehensive requirement can be met by taking Biomolecular Engineering 211, Computational Systems Biology; 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.
Requirements of 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)
Biology 20A, Cell and Molecular Biology; and
One of the following:
Biology 20B, Development and Physiology; or
Biology 110, Cell Biology; or
Biology 105, Genetics; or
Biology 115, Eukaryotic Molecular Biology; or
Biology 119, Microbiology
General chemistry (3)
Chemistry 1A, 1B/M, and 1C/N
Single-Variable Calculus (2)
Mathematics 19A and 19B (preferred); or
Mathematics 11A and 11B; or
Mathematics 20A and 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 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 112B
Biochemistry (1)
Biochemistry 100A; or
Chemistry 103; 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 pursuing 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./graduate degree 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 230, Computational Genomics
Applied Mathematics and Statistics 206, Bayesian Statistics
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 are automatically included in the combined B.S./M.S. or B.S./Ph.D. program.
Bioinformatics Major Planners
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 or bioinformatics degree should follow the biomolecular engineering 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 laboratories in the summer after completing general chemistry, so that biochemistry may be started in the junior year.
Biomolecular Engineering 205, Bioinformatics Models and Algorithms, should be taken after Biomolecular Engineering 110, Computational Biology Tools.
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Sample Plan |
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Year |
Fall |
Winter |
Spring |
|
1st |
MATH 19A |
MATH 19B |
MATH 23A |
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CHEM 1A |
CHEM 1B/M |
CHEM 1C/N |
|
|
college core |
gen ed |
gen ed |
|
|
2nd |
BIOL 20A |
CMPS 12A/L |
CMPS 12B/M |
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CHEM 108A/L |
BIOL 105 |
CMPE 16 |
|
|
BME 80G |
gen ed |
gen ed |
|
Biomolecular Engineering and Bioinformatics Graduate Program
The Department of Biomolecular Engineering offers interdisciplinary M.S. and Ph.D. degrees in biomolecular engineering and bioinformatics.
Course Requirements
Both masters and doctoral students must complete eight, 5-credit courses and one 3-credit research and teaching course. In addition, M.S. students must complete three seminar courses, while Ph.D. students must complete five seminar courses. M.S. students must also complete one lab rotation, and Ph.D. students must complete three research laboratory rotations (course 296) with different supervisors.
Core courses (5-credit) six are required
Bioinformatics Emphasis
Biomolecular Engineering 205, Bioinformatics Models and Algorithms
Two Biomolecular Engineering graduate courses from the bioinformatics list
One Biomolecular Engineering graduate course from the biomolecular engineering list
One graduate statistics course (Applied Mathematics and Statistics 206B recommended)
One graduate course from MCD Biology, Chemistry and Biochemistry, or Microbiology and Environmental Toxicology
Biomolecular Engineering Emphasis
Biomolecular Engineering 207, Molecular Recognition
Two Biomolecular Engineering graduate course from the biomolecular engineering list (BME 205B recommended)
One Biomolecular Engineering graduate courses from the bioinformatics list
Two graduate courses from Applied Mathematics and Statistics, MCD Biology, Chemistry and Biochemistry, or Microbiology and Environmental Toxicology
Ethics Course (5-credit) one is required
Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society; or Philosophy 245, Brave New World: Ethical Issues in Genetics; or Biomolecular Engineering 247, Stem Cell Research; Scientific, Ethical, Social and Legal Issues, or Sociology 268A, Science and Justice: Experiments in Collaboration.
Electives (5-credit) one is required
One graduate course consistent with the students degree objectives. With preapproval by the graduate director, this elective may be an upper-division undergraduate course selected to improve background in areas not studied as an undergraduate.
Independent or thesis research courses cannot be counted as electives.
Students must choose courses with faculty guidance and approval to balance their preparation and make up for deficiencies in background areas. With consent of the graduate director, variations in the composition of the required courses may be approved.
Other Curriculum Requirements
Biomolecular Engineering 200, Research and Teaching in Bioinformatics, 3 credits
Seminars
M.S. students: a minimum of three seminar courses, including at least one quarter of the 2-credit Biomolecular Engineering seminar, 280B
Ph.D. students: a minimum of six seminar courses, including at least two quarters of the 2-credit Biomolecular Engineering seminar, 280B
Before and after advancement, full-time Ph.D. students are required to enroll in at least one seminar course each quarter (e.g., 280 or 281), and must present the results of their ongoing research at least once each year. Because the intent of the seminar requirement is to ensure breadth of knowledge, lab group meetings (BME 281 courses) do not count for the seminar requirement.
Research Experience
M.S. students: one lab rotation research project.
Ph.D. Students: three quarters of laboratory rotations (course 296), generally within the first 12 months. One of the laboratory rotations must be with a faculty supervisor who does wet-lab research, though the students rotation project may be purely computational.
Course Lists
The following are the bioinformatics and biomolecular engineering course lists. The lists are subject to change as courses and course content changes. The graduate office maintains the current list.
Bioinformatics list: 205, 211, 225, 230, 235
Biomolecular Engineering list: 207, 210, 215, 222, 250, 255
Qualifying Examinations
Ph.D. students are required to pass an oral qualifying examination by the end of their second year and to advance to candidacy by the end of their third year. Students advancing to candidacy by the end of their second year have the oral exam requirement waived.
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.
Masters Capstone Requirement
M.S. students must complete a one-quarter research project with written report to fulfill the capstone requirement. Most often, this requirement is satisfied with Biomolecular Engineering 296 or Biomolecular Engineering 297.
Doctoral Dissertation Requirements
Ph.D. students must pass an oral comprehensive examination 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 which is approved by the graduate director and the campus graduate dean. At least two of the four must be members of the Department of Biomolecular Engineering. 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.
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 graduate director upon the recommendation of the dissertation supervisor. At least one of the three must be a member of the Department of Biomolecular Engineering. 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.
Revised: 09/01/13
