Biomolecular Engineering
Lower-Division Courses
The following courses are offered under the subject area of Biomolecular Engineering (BME).60. Programming
for Biologists and Biochemists. S
Lecture and lab-based course teaching programming skills needed by biologists
and biochemists. No programming experience required, but basic computer
skills assumed. Students without prior programming experience will be
given the basic proficiency in Perl, BioPerl, and other Perl libraries
needed to analyze, transform, and publish biological data. Prerequisite(s):
Biology 20A or 21A. (General Education Codes: Q, IN.) C. Rohl
80G. Bioethics in the Twenty-First Century: Science, Business,
and Society. W
Serves science and non-science majors interested in bioethics. Guest speakers
and instructors lead discussions of major ethical questions having arisen
from research in genetics, medicine, and industries supported by this
knowledge. (Also offered as Chemistry and Biochemistry 080G. Students
cannot receive credit for both courses.) (General Education Code: T2-Natural
Sciences.) D. Deamer, E. Suckiel
Upper-Division Courses
100. Introduction to Bioinformatics.
F
Introduction to bioinformatics, the use of computational techniques to
convert the masses of information from biochemical experiments (DNA sequencing,
DNA chips, and other high-throughput experimental methods) into useful
information. The emphasis is on DNA and protein sequence alignment and
analysis. Prerequisite(s): Computer Science 12B; Computer Engineering
107 or Engineering 131; concurrent enrollment in course 100L required.
Corequisite: Biochemistry 100A. Enrollment limited to 30. K. Karplus
100L. Introduction to Bioinformatics Laboratory (1 credit). F
Introduction to bioinformatics, the use of computational techniques to
convert the masses of information from biochemical experiments (DNA sequencing,
DNA chips, and other high-throughput experimental methods) into useful
information. The emphasis is on DNA and protein sequence alignment and
analysis. Prerequisite(s): Computer Science 12B; Computer Engineering
107 or Engineering 131; concurrent enrollment in course 100 required.
Corequisite: Biochemistry 100A. Enrollment limited to 30. K. Karplus
110. Computational Biology Tools. F
Hands-on laboratory geared to teach basic tools used in computational
biology (motif searching, primer selection, sequence comparison, multiple
sequence alignment, genefinders, phylogenetics analysis, X-ray crystallography
software). Web- and Unix-based tools/databases are used. Open to all science
students; no prior Unix experience required. Prerequisite(s): Biology
100 or Biochemistry 100A. Enrollment limited to 25. T. Lowe
193. Field Study. F,W,S
Provides for individual programs of study with specific aims and academic
objectives carried out under the direction of a BME faculty member and
a willing sponsor at a field site, using resources not normally available
on campus. Credit is based upon written and oral presentations demonstrating
the achievement of the objectives of the course. Prerequisite(s): Petition
on file with sponsoring agency. Enrollment restricted to Bioinformatics
majors. The Staff
193F. Field Study (2 credits). F,W,S
Provides for individual programs of study with specific aims and academic
objectives carried out under the direction of a BME faculty member and
a willing sponsor at a field site, using resources not normally available
on campus. Credit is based upon written and oral presentations demonstrating
the achievement of the objectives of the course. Prerequisite(s): Petition
on file with sponsoring agency. Enrollment restricted to Bioinformatics
majors. The Staff
194. Group Tutorial. F,W,S
A program of study arranged between a group of students and a faculty
member Prerequisite(s): Petition on file with sponsoring agency. Enrollment
restricted to Bioinformatics majors. May be repeated for credit. The
Staff
194F. Group Tutorial (2 credits). F,W,S
A program of independent study arranged between a group of students and
a faculty member Prerequisite(s): Petition on file with sponsoring agency.
Enrollment restricted to Bioinformatics majors. May be repeated for credit.
The Staff
195. Senior Thesis Research. F,W,S
Prerequisite(s): Petition on file with sponsoring agency. Enrollment restricted
to Bioinformatics majors. May be repeated for credit. The Staff
195F. Senior Thesis or Research (2 credits).
Prerequisite(s): Petition on file with sponsoring agency. Enrollment restricted
to Bioinformatics majors. May be repeated for credit. The Staff
198. Individual Study or Research. F,W,S
Prerequisite(s): Petition on file with sponsoring agency. Enrollment restricted
to Bioinformatics majors. May be repeated for credit. The Staff
198F. Individual Study or Research (2 credits). F,W,S
Prerequisite(s): Petition on file with sponsoring agency. Enrollment restricted
to Bioinformatics majors. May be repeated for credit. The Staff
199. Tutorial. F,W,S
For fourth-year students majoring in bioinformatics Enrollment restricted
to Bioinformatics majors. May be repeated for credit. The Staff
Graduate Courses
200. Research and Teaching in Bioinformatics (3 credits). FBasic teaching techniques for teaching assistants, including responsibilities and rights of teaching assistants, resource materials, computer security, leading discussion or lab sessions, presentation techniques, maintaining class records, electronic handling of homework, and grading. Examines research and professional training, including use of library and online databases, technical typesetting, writing journal and conference papers, publishing in bioinformatics, giving talks in seminars and conferences, and ethical issues in science and engineering. Required for all teaching assistants. Enrollment restricted to graduate students. K. Karplus, T. Lowe, C. Rohl
220. Protein Bioinformatics. W
Covers the application of bioinformatics techniques to protein sequences and structures. Topics include protein sequence analysis, protein structure prediction, and sources of experimental data about proteins. A substantial project is required. Prerequisite(s): courses 100 and 100L. Enrollment restricted to graduate students; undergraduates may enroll if they have completed course 100, Computer Science 101, and Biochemistry and Molecular Biology 100A; or by permission of the instructor. (Formerly Computer Science 243.) C. Rohl
230. Computational Genomics. S
Genomics databases: analysis of high-throughput genomics datasets; BLAST and related sequence comparison methods; pairwise alignment of biosequences by dynamic programming; statistical methods to discover common motifs in biosequences; multiple alignment and database search using motif models; constructing phylogenetic trees; hidden Markov models for finding genes, etc.; discriminative methods for analysis of bioinformatics data, neural networks, and support vector machines; locating genes and predicting gene function, including introduction to linkage analysis and disease association studies using SNPs; and modeling DNA and RNA structures. Prerequisite(s): courses 100 and 100L. Enrollment restricted to graduate students; undergraduates may enroll if they have completed course 100, Computer Science 101, and Biochemistry and Molecular Biology 100A; or by permission of the instructor. (Formerly Computer Science 244.) T. Lowe
280B. Seminar on Bioinformatics (2 credits). F
Weekly seminar series covering topics of current research in computational biology or bioinformatics. Current research work and literature in these areas are discussed in weekly meetings. Enrollment restricted to graduate students or permission of instructor. (Formerly Computer Engineering 280B.) May be repeated for credit. C. Rohl, K. Karplus
297. Independent Study or Research. F,W,S
Independent study or research under faculty supervision. Although course may be repeated for credit, not every degree program accepts a repeated course towards degree requirements. Prerequisite(s): petition on file with sponsoring agency. May be repeated for credit. The Staff
299. Thesis Research. F,W,S
Thesis research conducted under faculty supervision. Although course may be repeated for credit, not every degree program accepts a repeated course towards degree requirements. Prerequisite(s): petition on file with sponsoring agency. May be repeated for credit. The Staff