Biomolecular Engineering
2014-15 General Catalog
Baskin School of Engineering
335 Baskin Engineering Building
(831) 459-2158
http://www.soe.ucsc.edu
Lower-Division Courses
5. Introduction to Biotechnology. F,W,S
Introduces the tools and applications of biotechnology in the fields of medicine, agriculture, the environment, and industry. (General Education Code(s): PE-T, IN.) W. Rothwell, 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): PE-T, T6-Natural Sciences or Humanities and Arts.) M. Akeson, S. Dreisbach, The Staff
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. (General Education Code(s): PE-T, T2-Natural Sciences.) W. Rothwell, The Staff
88A. BMES Freshman Design Seminar (2 credits). W
A first course in engineering design for bioengineers. In cooperation with the Biomedical Engineering Society (BMES). Students choose a design project and work on it in competitive and cooperative teams. Covers research, design, prototyping, and report writing. Enrollment restricted to freshman majors and proposed majors in Bioengineering. Enrollment limited to 25. (General Education Code(s): PR-E.) K. Karplus
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
101. Applied Circuits for Bioengineers. S
Introduces analog electronics. Topics include circuit theory (Kirchoff's laws, Thevenin equivalents); constant and sinusoidal signals; RC filters op amps; feedback; oscillators; and instrumentation amplifiers. Emphasis is on design for sensors (thermistors, microphones, electrodes, pressure sensors, phototransistors); voltage dividers are a recurring theme. Prerequisite(s): Mathematics 11B, 19B, or 20B and Physics 5C/N or 6C/N which may be taken concurrently with Biomolecular Engineering 101. K. Karplus
101L. Applied Circuits Laboratory (2 credits). S
Twice weekly, three-hour laboratory to design and build circuits to interface sensors used in bioengineering (thermistors, microphones, electrodes, pressure sensors, phototransistors). Students design and build a one-lead electrocardiograph (EKG). Students are billed a materials fee. Prerequisite(s): Physics 5C/N or 6C/N. Concurrent enrollment in course 101 is required. Enrollment limited to 48. K. Karplus
110. Computational Biology Tools. F,W
Hands-on lectures and laboratory geared to teach basic tools and skills used in computational biology (genome browsers, sequence database searching, motif analysis, multiple sequence alignment, gene finders, phylogenetics analysis, protein structure visualization, and others). Web-based tools/databases are used on student laptops. Open to all science students; no prior programming or Unix experience required. (Also offered as Biology: Molecular Cell & Dev 181. Students cannot receive credit for both courses.) Prerequisite(s): Biology 100, 105, Biochemistry 100A, or Chemistry 103 or declared Bioinformatics majors. Enrollment limited to 25. T. Lowe, The Staff
123A. Bioengineering Project 1 (7 credits). F
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. Students are billed a materials fee. Prerequisite(s): course 140 or 150 and previous or concurrent enrollment in Computer Engineering 185. Enrollment restricted to biogengineering majors. (General Education Code(s): PR-E.) The Staff, M. Akeson, K. Karplus
123B. Bioengineering Project 2 (7 credits). W
Second of two-course bioengineering project sequence. Students implement and test the engineering designs from course 123A. Projects are usually done as group projects, but individual projects are permitted. Requires written progress reports, formal written report, and oral presentation before a panel of faculty. Students are billed a materials fee. Prerequisite(s): course 123A and Computer Engineering 185. Enrollment restricted to biogengineering majors. Enrollment limited to 30. M. Akeson, The Staff
123T. Senior Thesis Presentation (2 credits). W
For bioengineering senior thesis students, guidance in preparing a research seminar and a draft manuscript describing their senior research project. Students collaborate with each other and with investigators from their sponsoring laboratory as they fulfill the course requirements. Prerequisite(s): Computer Engineering (CMPE) 185. Concurrent enrollment in BME 193 or BME 195 or BME 198 or CMPE 193 or CMPE 195 or CMPE 198 or Electrical Engineering (EE) 193 or EE 195 or EE 198 is required. Enrollment limited to 25. (General Education Code(s): PR-E.) The Staff, M. Akeson, K. Karplus
128. Protein Engineering. S
For bioengineering, bioinformatics, and biology majors, focuses on engineering (i.e., changing) of proteins. Topics focus on practical aspects of protein engineering strategies that are crucial to modern biotechnology and biomedicinal applications. Prerequisite(s): Biology 20A, and Biology 100 or Biochemistry and Molecular Biology 100A, or by permission of instructor. R. Dubois, The Staff
130. Genomes. F,S
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. (Also offered as Biology: Molecular Cell & Dev 182. Students cannot receive credit for both courses.) Prerequisite(s): Biology 100 or Chemistry 103 or Biochemistry 100A; and Biology 105; or approval of instructor. Enrollment limited to 30. R. Green
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). Students are billed a materials fee. 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. M. Akeson
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 Biomolecular Engineering 255 and Chemistry 255. (Also offered as Biology: Molecular Cell & Dev 179. Students cannot receive credit for both courses.) Prerequisite(s): Biology 20A and Biology 100 or Chemistry 103 or Biochemistry and Molecular Biology 100A. Enrollment limited to 15. P. Berman
160. Research Programming in the Life Sciences. S
No programming experience is required, but basic computer and molecular biology understanding is assumed. Students learn programming in Python to manipulate biological data. Programming assignments comprise the majority of the assignments, and a final project using skills developed in this course is required. BioPython and other modules introduced for use in the final project. (Formerly Research Programming for Biologists and Biochemists.) (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. (General Education Code(s): MF.) J. Stuart, The Staff
160L. Research Programming in the Life Sciences Laboratory (1 credit). S
Laboratory sequence illustrating topics covered in course 160. One two-hour laboratory per week. (Formerly Research Programming for Biologists and Biochemists Laboratory.) (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. J. Stuart, The Staff
170. Drug Action and Development. S
Lectures and case studies explore principles and approaches in drug discovery and development, emphasizing concepts in pharmacology; medicinal chemistry; and genomics- and bioinformatics-based approaches to drug discovery to illustrate pathways from discovery through development for clinical use. Cannot receive credit for this course and course 270. (Formerly Frontiers in Drug Action and Discovery.) (Also offered as Chemistry and Biochemistry 170. Students cannot receive credit for both courses.) Prerequisite(s): Biology 100 or Chemistry 103 or Biochemistry 100A. Biology 110 and 130/L or 131/L are recommended. Enrollment restricted to juniors and seniors. D. Smith, T. Holman, M. Camps, R. Linington, P. Berman
177. Engineering Stem Cells. W
For bioengineering students interested in stem cells. Class uses project-based learning to discuss basic stem cell concepts and past breakthrough approaches to identify and design solutions for technological hurdles in stem cell research. Prequisite(s): course 140 or 150, and BIOL 100, or by consent of instructor. Enrollment limited to 30. C. Forsberg
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. May be repeated for credit. 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. May be repeated for credit. 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. May be repeated for credit. The Staff
195F. Senior Thesis or Research (2 credits). F,W,S
Students submit petition to sponsoring agency. May be repeated for credit. The Staff
198. Individual Study or Research. F,W,S
Students submit petition to sponsoring agency. May be repeated for credit. The Staff
198F. Individual Study or Research (2 credits). F,W,S
Students submit petition to sponsoring agency. May be repeated for credit. The Staff
199. Tutorial. F,W,S
For fourth-year students majoring in bioinformatics or bioengineering. 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. 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
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
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 by instructor permission if they have completed course 205, Computer Science 101, BIOC 100A. J. Stuart, R. Green, D. Haussler
230L. Computational Genomics Laboratory (1 credit). W
Project in computational genomics. Prerequisite(s): course 205; concurrent enrollment in course 230 is required. J. Stuart, R. Green, D. Haussler
235. Banana Slug Genomics.
Students will assemble and annotate the banana slug genome (Ariolimax dolichophallus) from next-generation sequencing data. Students also will explore the capabilities of the latest next-generation bioinformatics tools and write their own as needed. Prerequisite(s): course 205 or graduate status. Seniors who have taken course 110 and a computer programming course may enroll with permission of instructor. May be repeated for credit. K. Karplus, The Staff
237. Applied RNA Bioinformatics.
Teaches methods for RNA gene discovery; probabilistic modeling, secondary structure/trans-interaction prediction; mRNA splicing; and functional analysis. Emphasis on leveraging comparative genomics and employing high-throughput RNA sequencing data. Includes lectures, scientific literature discussion, problem sets, and final gene-discovery project. Enrollment restricted to seniors and graduate students. T. Lowe, The Staff
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. M. Akeson
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 and Biology 179. (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
268A. Science and Justice: Experiments in Collaboration. S
Considers the practical and epistemological necessity of collaborative research in the development of new sciences and technologies that are attentive to questions of ethics and justice. Enrollment by permission of instructor. Enrollment restricted to graduate students. (Also offered as Anthropology 267A, Feminist Studies 268A, and Sociology 268A. Students cannot receive credit for more than one course.) Enrollment limited to 15. The Staff
268B. Science and Justice Research Seminar.
Provides in-depth instruction in conducting collaborative interdisciplinary research. Students produce a final research project that explores how this training might generate research that is more responsive to the links between questions of knowledge and questions of justice. Prerequisite(s): Sociology 268A, Biomolecular Engineering 268A, Feminist Studies 268A, or Anthropology 267A. Enrollment by permission of instructor. Enrollment restricted to graduate students. (Also offered as Anthropology 267B, Feminist Studies 268B, and Sociology 268B. Students cannot receive credit for more than one course.) Enrollment limited to 15. The Staff
270. Drug Action and Development. S
Lectures and case studies explore principles and approaches in drug discovery and development, emphasizing concepts in pharmacology; medicinal chemistry; and genomics- and bioinformatics-based approaches to drug discovery to illustrate pathways from discovery through development for clinical use. Cannot receive credit for this course and course 170. (Formerly Frontiers in Drug Action and Discovery.) (Also offered as Chemistry and Biochemistry 270. Students cannot receive credit for both courses.) Enrollment restricted to graduate students. D. Smith, T. Holman, M. Camps, R. Linington, P. Berman
280B. Seminar on Bioinformatics and Bioengineering (2 credits). F,W,S
Weekly seminar series covering topics of current research in computational biology, and bioinformatics. Current research work and literature in these areas are discussed.(Formerly Seminar on Bioinformatics.) May be repeated for credit. The Staff
281A. Seminar on Processive Enzymes and Nanopores (2 credits). F,W,S
Weekly seminar series covering experimental research in nanopore technology and single-molecule analysis of polymerase function. Current research work and literature is 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. M. Akeson
281B. HIV Vaccine Research (2 credits). F,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
281C. Seminar in Cancer Genomics (2 credits). F,W,S
Presents current computational biology research to identify genomics-based signatures of cancer onset, progression, and treatment response. Examples of such investigations include: genetic pathway interpretation of multivariate high-throughput datasets; discovery of mutations in whole-genome sequence; identifications and quantification of gene isoforms, alleles, and copy number variants; and machine-learning tools to predict clinical outcomes. Students present their own research, host journal clubs, and attend lectures and teleconferences to learn about research conducted by national and international projects. Enrollment restricted to graduate students. May be repeated for credit. D. Haussler, J. Stuart
281E. Seminar in Genomics (2 credits). F,W,S
Current topics in genomia including high-throughput sequencing, genome assembly, and comparative genomics. Students design and implement independent research projects. Weekly laboratory meetings are held to discuss these projects and related research in the field. Enrollment restricted to graduate students May be repeated for credit. R. Green
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 restricted to graduate students. Undergraduates may enroll with permission of instructor. Enrollment limited to 10. May be repeated for credit. C. Forsberg
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). 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
281P. Seminar on Nanotechnology and Biosensors (2 credits). F,W,S
Weekly seminar covering topics of research in the development of new tools and technologies to detect and study genes and proteins. Latest research work and literature in these areas are 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. N. Pourmand
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
Revised: 09/01/14
