Biomolecular Engineering

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

Lower-Division Courses

60. Programming for Biologists and Biochemists. W
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 taught the basic proficiency in Perl, BioPerl, and other Perl libraries needed to analyze, transform, and publish biological data. Students cannot receive credit for this course and Biomolecular Engineering 160 or Biology 180. Prerequisite(s): Biology 20A or 21A. Previous or concurrent enrollment in course 60L required. J. Stuart, The Staff

60L. Programming for Biologists and Biochemists Laboratory (1 credit). W
Laboratory sequence illustrating topics covered in course 60. One two-hour laboratory per week. Concurrent enrollment in course 60 required. Students cannot receive credit for this course and Biomolecular Engineering 160L or Biology 180L. Prerequisite(s): Biology 20A or 21A. Previous or concurrent enrollment in course 60 is required. J. Stuart, The Staff

80G. Bioethics in the 21st Century: Science, Business, and Society. F
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 Philosophy 80G. Students cannot receive credit for both courses.) (General Education Code(s): T6-Natural Sciences or Humanities and Arts.) E. Suckiel, M. Akeson

80H. The Human Genome. F,W,S
Course will focus on understanding human genes. Accessible to non-science majors. Will cover principles of human inheritance and techniques used in gene analysis. The evolutionary, social, ethical, and legal issues associated with knowledge of the human genome will be discussed. (Also offered as Biology 80H. Students cannot receive credit for both courses.) (General Education Code(s): T2-Natural Sciences.) W. Rothwell, M. Ares

94. Group Tutorial. F,W,S
Provides a means for a small group of students to study a particular topic in consultation with a faculty sponsor. Students submit petition to sponsoring agency. May be repeated for credit. The Staff

94F. Group Tutorial (2 credits). F,W,S
Provides a means for a small group of students to study a particular topic in consultation with a faculty sponsor. Students submit petition to sponsoring agency. May be repeated for credit. The Staff

99. Tutorial. F,W,S
Students submit petition to sponsoring agency. May be repeated for credit. The Staff

99F. Tutorial (2 credits). F,W,S
Students submit petition to sponsoring agency. May be repeated for credit. The Staff

Upper-Division Courses

102. Introduction to Medical Biotechnology. S
Lecture course covering biotechnology-based approaches to diagnosis and treatment of disease. Areas covered include molecular diagnostics, microarray technology and pharmacogenomics, targeted therapies, gene therapy and cell and tissue engineering. Recent advances in each field presented. Prerequisite(s): Biology 20A, or Biology 21A, or Biomolecular Engineering/Biology 80H. W. Rothwell, The Staff

109. Resource-Efficient Programming. *
Writing programs that use computer resources efficiently. Learn to measure resource usage and modify programs to get better performance. Particularly appropriate for programmers working at limits of their hardware (bioinformaticians, game programmers, and embedded system programs). Prerequisites(s): Computer Science 12B and 12M or 13H and 13L, Computer Engineering 16 or 16H, and Mathematics 19A. Enrollment limited to 90. K. Karplus

110. Computational Biology Tools. S
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. (Also offered as Biology 181. Students cannot receive credit for both courses.) Prerequisite(s): Biology 20B and Chemistry 1C. Enrollment limited to 25. T. Lowe, The Staff

130. Genomes. *
Advanced elective for biology majors, examining biology on the genome scale. Topics include genome sequencing; large scale computational and functional analysis; features specific to prokaryotic, eukaryotic, or mammalian genomes; proteomics; SNP analysis; medical genomics; and genome evolution. Prerequisite(s): Biology 100 or Biochemistry 100A and Biology 105, or approval of instructor. Enrollment limited to 30. T. Lowe

160. Research Programming for Biologists and Biochemists. W
No programming experience required, but basic computer skills assumed. Students without prior programming experience taught basic proficiency in Perl, BioPerl, and other Perl libraries needed to analyze, transform, and publish biological data. Students required to solve a research problem as a final project. Lectures and labs are shared with course 60. Students cannot receive credit for this course and course 60. (Also offered as Biology 180. Students cannot receive credit for both courses.) Prerequisite(s): Biology 20A or 21A. Concurrent enrollment in course 180L is required. J. Stuart

160L. Research Programming for Biologists and Biochemists
Laboratory (1 credit). W
Laboratory sequence illustrating topics covered in course 160. One two-hour laboratory per week. Students cannot receive credit for this course and course 60L. (Also offered as Biology 180L. Students cannot receive credit for both courses.) Prerequisite(s): Biology 20A or 21A. Previous or concurrent enrollment in course 160 is required. J. Stuart, The Staff

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. Students submit petition to sponsoring agency. 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. Students submit petition to sponsoring agency. The Staff

194. Group Tutorial. F,W,S
A program of study arranged between a group of students and a faculty member. Students submit petition to sponsoring agency. 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. Students submit petition to sponsoring agency. May be repeated for credit. The Staff

195. Senior Thesis Research. F,W,S
Students submit petition to sponsoring agency. Enrollment restricted to bioinformatics majors. May be repeated for credit. The Staff

195F. Senior Thesis or Research (2 credits). F,W,S
Students submit petition to sponsoring agency. Enrollment restricted to bioinformatics majors. May be repeated for credit. The Staff

198. Individual Study or Research. F,W,S
Students submit petition to sponsoring agency. Enrollment restricted to bioinformatics majors. May be repeated for credit. The Staff

198F. Individual Study or Research (2 credits). F,W,S
Students submit petition to 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). F
Basic 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. T. Lowe, K. Karplus

205. Bioinformatics Models and Algorithms. F
Covers bioinformatics models and algorithms: 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. Emphasis is on DNA and protein sequence alignment and analysis. (Formerly course 100, Introduction to Bioinformatics.) Enrollment restricted to graduate students. Undergraduates may enroll with prerequisite(s): Computer Science 12B; and Computer Engineering 107 or Applied Math and Statistics 131; and Biology 20A; and concurrent enrollment in Biochemistry 100A. K. Karplus

210. Application and Analysis of Microarrays. S
Topics include, but are not limited to, microarray production techniques, experimental strategies using microarrays, extraction and analysis of microarray data, DNA and protein arrays, SNP analysis, gene expression analysis, materials analysis, and advanced analysis of data using bioinformatic techniques. (Also offered as Biology 210. Students cannot receive credit for both courses.) Enrollment restricted to graduate students; undergraduates by permission of instructor. M. Ares, T. Lowe

220. Protein Bioinformatics. S
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. Prerequisite(s): course 205, or Chemistry 200B; concurrent enrollment in course 220L, 296, or 297 is required. Enrollment restricted to graduate students; undergraduates may enroll if they have completed course 205, CMPS 101, and BIOC 100A. K. Karplus, The Staff

220L. Protein Bioinformatics Laboratory (1 credit). S
Project in protein bioinformatics. Prerequisite(s): course 205; concurrent enrollment in course 220 is required. K. Karplus, The Staff

230. Computational Genomics. W
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): course 205; concurrent enrollment in course 230L, 296, or 297 is required. Enrollment restricted to graduate students; undergraduates may enroll if they have completed course 205, Computer Science 101, and BIOC 100A. J. Stuart, D. Haussler, T. Lowe

230L. Computational Genomics Laboratory (1 credit). W
Project in computational genomics. Prerequisite(s): course 205; concurrent enrollment in course 230 is required. J. Stuart, D. Haussler, T. Lowe

280B. Seminar on Bioinformatics (2 credits). F,W,S
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. May be repeated for credit. J. Stuart, D. Haussler, T. Lowe, K. Karplus, D. Gerloff

281H. Seminar in Comparative Genomics (2 credits). F,W,S
Weekly seminar series covering topics of current computational and experimental research in comparative genomics. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. May be repeated for credit. D. Haussler

281K. Seminar on Protein Structure Prediction (2 credits). F,W,S
Weekly seminar series covering topics of current computational and experimental research in protein structure prediction. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. May be repeated for credit. K. Karplus

281L. Seminar in Computational Genetics (2 credits). F,W,S
Weekly seminar series covering topics and experimental research in computational genetics. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. May be repeated for credit. T. Lowe

281R. Seminar on Protein Structure and Function (2 credits). *
Weekly seminar series covering topics of current computational and experimental research in protein structure prediction and design, structure-function relationships and protein evolution. Current research work and literature in these areas discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualifed undergraduates may enroll with permission of instructor. May be repeated for credit. C. Rohl

281S. Seminar in Computational Functional Genomics (2 credits). F,W,S
Weekly seminar series covering topics of current computational and experimental research in computational functional genomics. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. May be repeated for credit. J. Stuart

293. Seminar in Biomolecular Engineering. W
Weekly seminar series covering topics of bioinformatics and biomolecular engineering research. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. The Staff

296. Research in Bioinformatics. F,W,S
Independent research in bioinformatics under faculty supervision. Although this course may be repeated for credit, not every degree program accepts a repeated course towards degree requirements.Students submit petition to sponsoring agency. May be repeated for credit. The Staff

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. Students submit petition to sponsoring agency. May be repeated for credit. The Staff

297F. Independent Study or Research (2 credits). 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. Students submit petition to sponsoring agency. Enrollment restricted to graduate students. May be repeated for credit. The Staff

299. Thesis Research. F,W,S
Thesis research conducted under faculty supervision. Although this course may be repeated for credit, not every degree program accepts a repeated course towards degree requirements. Students submit petition to sponsoring agency. May be repeated for credit. The Staff 

*Not offered in 2006-07