2016-17 General Catalog
Baskin School of Engineering
335 Baskin Engineering Building
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 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, an international 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 are required to take Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society to study the ethical, legal, and social implications of this new technology.
Program Learning Outcomes
A bioinformatics student completing the program should:
have a detailed knowledge of statistics, computer science, biochemistry, and genetics;
be able to find and use information from a variety of sources, including books, journal articles, and online encyclopedias;
be able to design and conduct computational experiments, as well as to analyze and interpret data;
be able to apply their knowledge to write programs for answering research questions in biology;
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.
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 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 80H, The Human Genome, covers principles of human inheritance and techniques used in gene analysis and discusses the evolutionary, social, ethical, and legal issues associated with knowledge of the human genome.
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 130, Genomes, teaches the principles of 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.
Biomolecular Engineering 160, Programming for Biologists and Biochemists, provides an introductory programming class using Python to analyze, transform, and publish biological data.
Declaration of the Major
Admission to the bioinformatics major is based on the required lower-division courses: BIOL 20A, BIOE 20B, BME 80G, CHEM 1A, CHEM 1B/M, CHEM 1C/N, CHEM 8A, CHEM 8B, CMPE 16, CMPS 12A/L (or CMPS 5J and 11 OR CMPE 12/L and CMPE 13/L), CMPS 12B/M, MATH 19A, MATH 19B, MATH 23A, and fundamental upper-division courses: AMS 131, and CMPS 101. Students must have completed 50 credits from this list by the end of the fifth quarter. Students must also have a GPA of 2.8 or better in all attempts in these courses. Students changing major after the sixth quarter will need 10 additional credits for each additional quarter.
Denials of admission to the major may be appealed by submitting a letter to the School of Engineering Undergraduate Office, describing why the grade point average obtained is not an accurate reflection of the student’s potential, or requesting that other completed upper-division courses be considered in admissions process.
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 receive "Highest Honors in the Major." Students with a GPA of 3.3 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.
Transfer students need eight transferable courses from the list of courses used for admission to the major for on-campus students, with a GPA in those courses of 2.8 or better. Students with fewer than 10 transferable courses may find it difficult to complete the major in only two more years.
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.
Majors must complete the following lower-division courses:
Biology (BIOL) 20A, Cell and Molecular Biology
Biology (BIOE) 20B, Development and Physiology
Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society
Chemistry 1A, 1B/M, and 1C/N, General Chemistry/Laboratory
Chemistry 8A and 8B, Organic Chemistry
Computer Engineering 16, Applied Discrete Mathematics
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
Computer Science 12B/M, Introduction to Data Structures/Laboratory
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
Majors must complete the following upper-division courses:
Applied Mathematics and Statistics
Applied Mathematics and Statistics 131, Introduction to Probability Theory
Applied Mathematics and Statistics 132, Statistical Inference
Biochemistry and Molecular Biology
Biochemistry 100A, Biochemistry (first in three-part sequence)
Biomolecular Engineering 110, Computational Biology Tools
Biomolecular Engineering 130, Genomes
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 105, Genetics
Computer Engineering 185, Technical Writing for Computer Engineers; or
Biomolecular Engineering 185, Technical Writing for Biomolecular Engineers
Computer Science 101, Algorithms and Abstract Data Types
Computer Science 109, Advanced Programming or BME 160/L, Research Programming in the Life Sciences
One of the following:
Computer Science 182, Introduction to Database Management Systems, or
Computer Science 180, Database Systems
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, or Biomolecular Engineering 185, Technical Writing for Biomolecular Engineers.
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.
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 20A, Cell and Molecular Biology; and
Biology 20B, Development and Physiology
General chemistry (3)
Chemistry 1A, 1B/M, and 1C/N
Organic chemistry (1)
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 5J and 11; or
Computer Engineering 12/L and 13/L
Biomolecular Engineering 80G
Upper-division (5 courses)
Biochemistry 100A; or
Chemistry 103; or
Programming 2 (1)
Biomolecular Engineering 160/L
Computer Engineering 107; or
Applied Mathematics and Statistics 131
Applied Mathematics and Statistics 132
Biomolecular Engineering 110
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 three courses in common:
Biomolecular Engineering 80G, Bioethics in the 21st Century
Biomolecular Engineering 205, Bioinformatics Models and Algorithms
Biomolecular Engineering 230, Computational GenomicsThe combined B.S./graduate degree program does not make any changes to the undergraduate program, except that students must pass the three overlapping courses listed above for a grade of B- or better.
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 undecided about 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. 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.
|gen ed||BIOE 20B||gen ed|
|BME 205||BME 230/L||CMPS 109|
|BME 130||CMPS 180||gen ed|
|gen ed||BME 185||gen ed|
Also note that a minimum of 35 credits (up to 15 can be upper-division, the rest graduate level) must be taken following the B.S..
Biomolecular Engineering and Bioinformatics Graduate Program
The Department of Biomolecular Engineering offers interdisciplinary M.S. and Ph.D. degrees in biomolecular engineering and bioinformatics.
Both masters and doctoral students must complete seven, 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 independent study (course 297), and Ph.D. students must complete three research laboratory rotations (course 296) with different supervisors. Lab rotations for Ph.D. students are generally completed in the first two quarters (three 7-week rotations). Ph.D students must also complete one 3-credit scientific writing course in their second year.
Core courses (5-credit) six are required
BME 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
Two Biomolecular Engineering graduate course from the biomolecular engineering list
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
*BME 80G, Bioethics in the Twenty-First Century: Science, Business, and Society
Sociology 268A, Science and Justice: Experiments in Collaboration.
*BME 80G can be taken to meet the ethics requirement, however, the credits will not be counted toward the overall credit requirement for the M.S. or Ph.D. since it is a lower-division course.
No electives are required. However, with faculty guidance students often choose to take upper-division undergraduate courses or graduate courses outside the department to make up for deficiencies in background areas of particular importance.
With consent of the graduate director, variations in the composition of the required courses may be approved.
Other Curriculum Requirements
BME 200, Research and Teaching in Bioinformatics, 3 credits
BME 201, Scientific Writing, 3 credits (Ph.D. only)
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.
M.S. students: one quarter of independent study (BME 297).
Ph.D. Students: three research laboratory rotations (course 296) with different supervisors. Lab rotations for Ph.D. students are generally completed in the first two quarters (three 7-week rotations). 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.
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, 230, 235
Biomolecular Engineering list: 215, 233, 255
Ph.D. students are required to pass the qualifying examination and advance to candidacy by the end of their second year.
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. In consultation with the faculty adviser, the student forms a Master’s Capstone Reading Committee of at least two faculty members (including the adviser), each of whom is provided a copy of the project report. The final project report must be signed by the reading committee before the award of the Master of Science Degree.
Doctoral Dissertation Requirements
Ph.D. students must select a faculty research adviser by the end of the first year. A qualifying examination committee is then formed in the second year, 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 program adviser 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.
Up to two courses may be transferred from other graduate institutions with the approval of the faculty adviser and the graduate director.