Biomolecular Engineering

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

Lower-Division Courses

60. Introductory 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. (Formerly Programming for Biologists and Biochemists.) Prerequisite(s): Biology 20A or 21A. Previous or concurrent enrollment in course 60L required. The Staff, J. Stuart

60L. Introductory 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. (Formerly Programming for Biologists and Biochemists Laboratory.) Prerequisite(s): Biology 20A or 21A. Previous or concurrent enrollment in course 60 is required. The Staff, J. Stuart

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.) M. Akeson, The Staff

80H. The Human Genome. F,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: Molecular Cell & Dev 80H. Students cannot receive credit for both courses.) (General Education Code(s): T2-Natural Sciences.) The Staff, 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

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. W,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: Molecular Cell & Dev 181. Students cannot receive credit for both courses.) Prerequisite(s): Biology 20B and Chemistry 1C Enrollment limited to 25. T. Lowe, D. Gerloff

123A. Engineering Design Project I. F,W
First of a two-course sequence that is the culmination of the engineering program. Students apply knowledge and skills gained in elective track to complete a major design project. Students complete research, specification, planning, and procurement for a substantial project. Includes technical discussions, design reviews, and formal presentations; engineering design cycle, engineering teams, and professional practices. Formal technical specification of the approved project is presented to faculty. Prerequisite(s): Electrical Engineering 171 or Computer Engineering 121; previous or concurrent enrollment in Computer Engineering 185; permission of department and instructor. Students are billed a materials fee. (Also offered as Electrical Engineering 123A and Computer Engineering 123A. Students cannot receive credit for all courses.) The Staff

123B. Engineering Design Project II (7 credits). *
Second of two-course sequence in engineering system design. Students fully implement and test system designed and specified in course 123A. Formal written report, oral presentation, and demonstration of successful project to review panel of engineering faculty required. Students are billed a materials fee. (Also offered as Electrical Engineering 123B and Computer Engineering 123B. Students cannot receive credit for all courses.) Prerequisite(s): course 123A and Computer Engineering 185. Enrollment limited to 35. 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

140. Bioinstrumentation. F
Introduction to theory, design, and application of bioinstrumentation in clinical, pharmaceutical, and biotechnology laboratories. Highly recommended for students planning careers in the biomolecular industries. Typical topics and demonstrations include thermocycler, polymerase chain reaction (PCR), pyrosequencing, fabless nanofabrication, ion-sensitive measurements, microarray fabrication, and fluorescent-activated cell sorter (FACS). Prerequisite(s): course 5, or Biology 100, or Biochemistry and Molecular Biology 100A. N. Pourmand

150. Molecular Biomechanics. S
Considers how assemblies of macromolecules (molecular motors) convert chemical energy into mechanical work on the nanometer-to-Angstrom scale. Processes examined include ATP-dependent movement of organelles in the cytocsol facilitated by kinesin; proton pumping by ATPases in the mitochondrial membrane; viral genome packaging; bacterial movement driven by flagella; processive addition of nucleotides by polymerases during replication and transcription; and protein synthesis by ribosomes. Cannot receive credit for this course and course 250. Prerequisite(s): Biology 20A; and Biology 20B or 105; and Biology 100 or Biochemistry 100A; and Physics 5C or 6C. Concurrent enrollment in course 150L required. H. Wang, M. Akeson, W. Dunbar

150L. Molecular Biomechanics Laboratory (2 credits). S
Students address a current scientific question about molecular motor function using techniques established in the UCSC Nanopore Laboratory. Specifically, students use recombinant DNA technology to produce an enzyme (e.g., a DNA polymerase) bearing a point mutation that is predicted to alter function in a defined manner. Students then use nanopore force spectroscopy to model the energy landscape for a mechanical or chemical step altered by the critical amino acid. Cannot receive credit for this course and course 250L. Prerequisite(s): Biology 20A; and Biology 20B or 105; and Biology 100 or Biochemistry 100A; and Physics 5C or 6C. Concurrent enrollment in course 150 required. H. Wang, M. Akeson, W. Dunbar

155. Biotechnology and Drug Development. W
Recommended for students interested in careers in the biopharmaceutical industry. Focuses on recombinant DNA technology and the drug-development process, including discovery research; preclinical testing; clinical trials; and regulatory review, as well as manufacturing and production considerations. Students may not receive credit for this course and course 255. (Also offered as Biology: Molecular Cell & Dev 179. Students cannot receive credit for both courses.) Prerequisite(s): Biology 20A and Biology 100 or Biochemistry and Molecular Biology 100A. Enrollment limited to 15. P. Berman

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 Biomolecular Engineering 60. Students cannot receive credit for this course and Biomolecular Engineering 60. (Also offered as Biology: Molecular Cell & Dev 180. Students cannot receive credit for both courses.) Prerequisite(s): Biology 20A or 21A. Previous or concurrent enrollment in course 160L is required. The Staff, 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 Biomolecular Engineering 60L. (Also offered as Biology: Molecular Cell & Dev 180L. Students cannot receive credit for both courses.) Prerequisite(s): Biology 20A or 21A. Previous or concurrent enrollment in course 160 is required. The Staff, J. Stuart

178. Stem Cell Biology. W
Basic concepts, experimental approaches, and therapeutic potential are discussed. Students gain experience in reading the primary scientific literature. (Also offered as Biology: Molecular Cell & Dev 178. Students cannot receive credit for both courses.) Prerequisite(s): Biology 110; Biology 115 recommended. C. Forsberg

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. 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

207. Biomolecular Recognition. *
Course is the core biomolecular-engineering emphasis graduate course. Focuses on the molecular mechanism enabling the flow of information within and between cells in living systems, and its application to engineering new tools for high-throughput molecular-biology research, improving biomedical diagnostics, and aiding treatment of human disease. Prerequisite(s): Equivalent of one full year of undergraduate biochemistry. Enrollment restricted to graduate students. T. Lowe, D. Gerloff, C. Forsberg, N. Pourmand

210. Experimental Systems Biology. F
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. (Formerly Application and Analysis of Microarrays.) (Also offered as Biology: Molecular Cell & Dev 210. Students cannot receive credit for both courses.) Enrollment restricted to graduate students; undergraduates by permission of instructor. T. Lowe

211. Computational Systems Biology. S
Teaches machine-learning methods relevant for the analysis of high-throughput molecular biology experiments. Students should be fluent in a programming language and should have taken basic molecular biology courses. Prerequisite(s): course 205. Enrollment restricted to graduate students; undergraduates may enroll if they have completed course 205, Computer Science 101, and any upper-division molecular biology or biochemistry course, such as Biochemistry 100 or 100A. J. Stuart

215. Applied Gene Technology. S
Detailed insight into the techniques and technological trends in genomics and transcriptomics, building the necessary foundations for further research in genetic association studies, population genetic association studies, population genetics, diagnostics, medicine, and drug development. Students should already have a deeper understanding of the basic tools of molecular biotechnology than acquired in introductory courses in biotechnology, biochemistry, and molecular biotechnology. Enrollment restricted to graduate students. N. Pourmand

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 and Biochemistry 100A. K. Karplus

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

222. Applied Biotechnology: Protein and Cell Engineering. S
For students interested in careers in the biotech industry. Focus is applied technology, with particular emphasis on the application of cell engineering and protein engineering to solve problems encountered in the design and manufacturing of biopharmaceutical products and industrial enzymes produced by recombinant DNA technology. Prior course work in biochemistry, molecular biology, genetics, and cell biology highly recommended. Enrollment restricted to graduate students; undergraduates may enroll with permission of instructor. P. Berman

225. Protein Function in Biology and Bioinformatics. F
Reviews functional roles of proteins and computational methods used to predict functional aspects of proteins. Focus is on molecular function and structure-function relationships. Wider-reaching notions of function (pathways, interaction networks) are considered peripherally, as the context in which molecular function occurs. Course includes lectures, (computational) lab work, and discussions of topical publications. Prerequisite(s): Biochemistry and Molecular Biology 100A (or equivalent knowledge) and courses 205 and 220, or by instructor's permission. Enrollment limited to 15. D. Gerloff

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

247. Stem Cell Research: Scientific, Ethical, Social, and Legal Issues. *
Scientific, ethical, social, and legal dimensions of human embryonic stem-cell research, including the moral status of the embryo; the concept of respect for life; ethical constraints on oocyte procurement; creation of embryonic chimeras; federal policies; and political realities. (Also offered as Biology: Molecular Cell & Dev 288. Students cannot receive credit for both courses.) Enrollment restricted to graduate students. E. Suckiel

250. Molecular Biomechanics. S
Considers how assemblies of macromolecules (molecular motors) convert chemical energy into mechanical work on the nanometer-to-Angstrom scale. Processes examined in the course include ATP-dependent movement of organelles in the cytocsol facilitated by kinesin; proton pumping by ATPases in the mitochondrial membrane; viral genome packaging; bacterial movement driven by flagella; processive addition of nucleotides by polymerases during replication and transcription; and protein synthesis by ribosomes. Cannot receive credit for this course and course 150. Enrollment restricted to graduate students. Concurrent enrollment in course 250L required. H. Wang, M. Akeson, W. Dunbar

250L. Molecular Biomechanics Laboratory (2 credits). S
Laboratory course taken in conjunction with course 250. Students address a current scientific question about molecular motor function using techniques established in the UCSC Nanopore Laboratory. Specifically, students use recombinant DNA technology to produce an enzyme (e.g., a DNA polymerase) bearing a point mutation that is predicted to alter function in a defined manner. Students then use nanopore force spectroscopy to model the energy landscape for a mechanical or chemical step altered by the critical amino acid. Cannot receive credit for this course and course 150L. Concurrent enrollment in course 250 required. Enrollment restricted to graduate students. H. Wang, M. Akeson, W. Dunbar

255. Biotechnology and Drug Development. W
Recommended for students interested in careers in the biopharmaceutical industry. Focuses on recombinant DNA technology and the drug-development process, including discovery research; preclinical testing; clinical trials; and regulatory review, as well as manufacturing and production considerations. Students may not receive credit for this course and Biomolecular Engineering 155. (Also offered as Chemistry and Biochemistry 255. Students cannot receive credit for both courses.) Enrollment limited to graduate students. Enrollment limited to 15. P. Berman

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, C. Forsberg, N. Pourmand

281B. HIV Vaccine Research (2 credits). F,W,S
Weekly seminar series covering topics of HIV vaccine 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. Enrollment limited to 10. May be repeated for credit. P. Berman

281F. Blood Cell Development (2 credits). F,W,S
Weekly seminar covering topics in current research on blood cell development and stem cell biology. Current research and literature in these areas discussed. Students lead some discussions and participate in all meetings. Enrollment restriced to graduate students. Undergraduates may enroll with permission of instructor. Enrollment limited to 10. May be repeated for credit. C. Forsberg

281G. Seminar on Protein Structure and Function (2 credits). F,W,S
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. (Formerly course 281R.) Enrollment restricted to graduate students; qualifed undergraduates may enroll with permission of instructor. May be repeated for credit. 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

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. *
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 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 2008-09