B.S Computer Science with a Specialization in Bioinformatics Course Descriptions
This page updated 8/24/2011.
Required Courses
Computer Science and Engineering Courses
CSE 8A. Introduction to Computer Science: Java (4)
Introductory computer science course designed for students interested in computing. No prior programming experience is assumed. Learn fundamental concepts of applied computer science using media computation. Must be taken concurrently with CSE 8AL. CSE 8A is part of a three-track course (CSE 8A, CSE 8AL, and CSE 8B) that is equivalent to CSE 11. Students should take CSE 8B to complete this track. Students who have taken CSE 8B or CSE 11 may not take CSE 8A. Recommended prep: High school algebra and familiarity with computing concepts. Prerequisites: corequisite of CSE 8AL.
CSE 8B. Introduction to Computer Science: Java (4)
Continuation of the Java language. Continuation of programming techniques. More on inheritance. Exception handling. CSE 8A is part of a three-track course (CSE 8A, CSE 8AL, and CSE 8B) that is equivalent to CSE 11. Students who have taken CSE 11 may not take CSE 8B. Recommended prep: High school algebra and familiarity with computing concepts. Prerequisites: CSE 8A and CSE 8AL.
CSE 11. Introduction to Computer Science and Object-Oriented Programming: Java (4)
An accelerated introduction to computer science and programming using the Java language. Basic UNIX. Modularity and abstraction. Documentation, testing and verification techniques. Basic object-oriented programming, including inheritance and dynamic binding. Exception handling. Event-driven and dynamic binding. Exception handling. Event-driven programming. Experience with AWT library or other similar library. Students who have completed CSE 8B may not take CSE 11. Recommended Prep: high-school algebra and familiarity with computing concepts and a course in a compiled language. Recommended prep: High school algebra and familiarity with computing concepts
CSE 12. Basic Data Structures and Object-Oriented Design (4)
Use and implementation of basic data structures including linked lists, stacks, and queues. Use of advanced structures such as binary trees and hash tables. Object-oriented design including interfaces, polymorphism, encapsulation, abstract data types, pre-/post-conditions. Recursion. Uses Java and Java Collections. Prerequisites: CSE 8B or CSE 11, and concurrent enrollment with CSE 15L.
CSE 21. Mathematics for Algorithms and Systems (4)
CSE 100. Advanced Data Structures (4) or Math 176. Advanced Data Structures (4) CSE 100 and Math 176 are identical courses.
CSE 100. Advanced Data Structures (4)
High-performance data structures and supporting algorithms. Use and implementation of data structures like (un)balanced trees, graphs, priority queues, and hash tables. Also memory management, pointers, recursion. Theoretical and practical performance analysis, both average case and amortized. Uses C++ and STL. Credit not offered for both Math 176 and CSE 100. Equivalent to Math 176. Prerequisites: CSE 21 or Math 15B or consent of instructor.
CSE 101. Design and Analysis of Algorithms (4)
Design and analysis of efficient algorithms with emphasis of non-numerical algorithms such as sorting, searching, pattern matching, and graph and network algorithms. Measuring complexity of algorithms, time and storage. NP-complete problems. Credit not offered for both Math. 188 and CSE 101. Equivalent to Math 188. Prerequisites: CSE 12, CSE 21 or Math. 15B or Math. 100A or Math. 103A.
Conjoined Bioinformatics Courses
CSE 181/BIMM 181/BENG 181. Molecular Sequence Analysis (4)
This course covers the analysis of nucleic acid and protein sequences, with an emphasis on the application of algorithms to biological problems. Topics include sequence alignments, database searching, comparative genomics, and phylogenetic and clustering analyses. Pairwise alignment, multiple alignment, DNS sequencing, scoring functions, fast database search, comparative genomics, clustering, phylogenetic trees, gene finding/DNA statistics. Prerequisites: CSE 100 or Math 176, CSE 101 or Math 188, BIMM 100 or Chem 114D. Bioinformatics majors only. CSE 181 is cross-listed with BIMM 181 and BENG 181.
CSE 182/BIMM 182/BENG 182/CHEM 182. Biological Databases (4)
This course provides an introduction to the features of biological data, how that data are organized efficiently in databases, and how existing data resources can be utilized to solve a variety of biological problems. Relational databases, object oriented databases, ontologies, data modeling and description, survey of current biological database with respect to above, implementation of a database focused on a biological topic. Prerequisites: CSE 100 or Math 176. Bioinformatics majors only. CSE 182 is cross-listed with BIMM 182, Chem 182, and BENG 182. Bioinformatics majors only.
BENG 183. Applied Genomic Technologies (4) Principles and technologies for using genomic information for biomedical applications. Technologies will be introduced progressively, from DNA to RNA to protein to whole cell systems. The integration of biology, chemistry, engineering, and computation will be stressed. Topics include: Technology for the Genome, DNA Chips, RNA Technologies, Proteomic Technologies, Physiomic and Phenomic Technologies, Analysis of Cell Function. Prerequisites: BIMM 100 or Chem 114C and BICD 110 or consent of department. Bioinformatics majors only.
CSE 184/BIMM 184/BENG 184. Computational Molecular Biology (4)
This advanced course covers the application of machine learning and modeling techniques to biological systems. Topics include gene structure, recognition of DNA and protein sequence patterns, classification, and protein structure prediction. Pattern discovery, Hidden Markov models/support victor machines/neural network/profiles. Protein structure prediction, functional characterization or proteins, functional genomics/proteomics, metabolic pathways/gene networks. Prerequisites: BIOINF 181, 182. Bioinformatics majors only.
BIMM 185. Bioinformatics Lab (4) This course emphasizes the hands-on application of bioinformatics methods to biological problems. Students will gain experience in the application of existing software, as well as in combining approaches to answer specific biological questions. Sequence alignment, fast database search, profiles and motifs, comparative genomics, gene finding, phylogenetic trees, protein structure, functional characterization of proteins, expression anaylysis, computational proteomics. This course open to bioinformatics majors only. Prerequisites: two courses out of BIMM 181 or BENG 181 or CSE 181, BIMM 182 or BENG 182 or CSE 182, BENG 183, BIMM 184 or BENG 184 or CSE 184. Attendance at the first lecture/lab is required. Nonattendance will result in the student’s being dropped from the course roster.Bioinformatics majors only.
Math 186. Probability Statistics for Bioinformatics (4)
This course will cover discrete and random variables, data analysis and inferential statistics, likelihood estimators and scoring matrices with applications to biological problems. Introduction to Binomial, Poisson, and Gaussian distributions, central limit theorem, applications to sequence and functional analysis of genomes and genetic epidemiology. (Credit not offered for Math 186 if Econ 120A, ECE 109, Math 180A, Math 181A, or Math 183 previously or concurrently.) Prerequisites: Math 20C (21C) with a grade of C– or better, or consent of instructor. Bioinformatics majors only.
Biology Courses
BILD 1. The Cell (4)
An introduction to cellular structure and function, to biological molecules, bioenergetics, to the genetics of both procaryotic and eucaryotic organisms, and to the elements of molecular biology. Three hours of lecture and one hour of recitation. Prerequisites: two quarters of general chemistry (second quarter of chemistry may be taken concurrently). (F,W,S)
BILD 2. Multicellular Life (4)
An introduction to the development and the physiological processes of plants and animals. Included are treatments of reproduction, nutrition, respiration, transport systems, regulation of the internal environment, the nervous system, and behavior. Three hours of lecture and one hour of recitation. Prerequisites: BILD 1. (F,W,S)
BILD 92. Professional Topics (1) (renumbered and revised to BILD 94)
This seminar will introduce students to the various subdisciplines and their research methodology in the biological sciences. Emphasis will be on bioinformatics, neurophysiology, and biotechnology. Current research topics in the specialized areas in academe and industry will be discussed. The role and professional identity of biologists in research, consulting, government, management, and teaching will be reviewed. In addition, issues surrounding professional ethics will be discussed.
BIBC 102. Metabolic Biochemistry (4) or Chem 114B Biochemical Energetics & Metabolism (4)
BIBC 102. Metabolic Biochemistry (4)
Energy-producing pathways–glycolysis, the TCA cycle, oxidative phosphorylation, photosynthesis, and fatty acid oxidation; and biosynthetic pathways–gluconeogenesis, glycogen synthesis, and fatty acid biosynthesis. Nitrogen metabolism, urea cycle, amino acid metabolism, nucleotide metabolism, and metabolism of macromolecules. Prerequisites: Chem 140A and Chem 140B. (Note: Students may not receive credit for both BIBC 102 and Chem 114B.)(F,W,S)
BIBC 103. Biochemical Techniques (4)
Introductory laboratory course in current principles and techniques applicable to research problems in biochemistry and molecular biology. Techniques include protein and nucleic acid purification; identification methods such as centrifugation, chromatography, and electrophoresis; immunological, spectrophotometric, and enzymatic methods. Prerequisites: BILD 1. Students may not receive credit for BIBC 103 after taking Chem 112A (renumbered to Chem 108). Attendance at the first lecture/lab is required. Nonattendance will result in the student’s being dropped from the course roster.
BIBC 110. Physical Biochemistry (4) or Chem 127 (Physical Chemistry) (4)
BIBC 110. Physical Biochemistry (4)
The structure and function of cells and cell organelles, cell growth and division, motility, cell differentiation and specialization. Prerequisites: BIBC 100 or BIBC 102.. (S)
BICD 100. Genetics (4)
An introduction to the principles of heredity in diploid organisms, fungi, bacteria, and viruses. Mendelian inheritance; population genetics; quantitative genetics; linkage; sex determination; meiotic behavior of chromosome aberrations, gene structure, regulation, and replication; genetic code. Three hours of lecture and one hour of recitation. Prerequisite: BILD 1 or the equivalent. (F,W,S)
BICD 110. Cell Biology (4)
The structure and function of cells and cell organelles, cell growth and division, motility, cell differentiation and specialization. Prerequisites: BIBC 100 or BIBC 102.
BIMM 100. Molecular Biology (4) or Chem 114D (Molecualr and Cellular Biochemistry) (4)
BIMM 100. Molecular Biology (4)
Molecular basis of biological processes, emphasizing gene action in context of entire genome. Chromo-somes and DNA metabolism: chromatin, DNA replication, repair, mutation, recombination, transposition. Transcription, protein synthesis, regulation of gene activity. Procaryotes and eucaryotes Prerequisites: BIBC 100 or BIBC 102, BICD 100. (Note: Students may not receive credit for both BIMM 100 and Chem. 114C.)
BIMM 101. Recombinant DNA Techniques (4) or Chem 112B (Recombinant DNA Lab) (4)
BIMM 101. Recombinant DNA Techniques (4)
Theory and practice of recombinant DNA and molecular biology techniques. Includes construction and screening of DNA libraries, DNA sequencing, PCR and its applications, bioinformatics, and RNA analysis. Prerequisites: BILD 1. Students may not enroll in or receive credit for both BIMM 101 and BIEB 123, or BIMM 101 and Chem 109 (formerly Chem 112B). BIMM 100 recommended. (F,W,S)
Chemistry Courses
Chem 6A. General Chemistry (4)
First quarter of a three-quarter sequence intended for science and engineering majors. Topics includes stoichiometry, gas laws, bonding, atomic theory, quantum theory, and thermochemistry. Three hours' lecture, one hour recitation. Prerequisites: proficiency in high school chemistry or physics. Math 1A (may be taken concurrently). (F,W,S)
Chem 6B. General Chemistry (4)
Second quarter of a three-quarter sequence intended for science and engineering majors. Topics include: molecular geometry, condensed phases and solutions, chemical equilibrium, acids and bases and thermodynamics. Three hours' lecture, one hour recitation. Prerequisites: Chem. 6A; Math. 20A or 1A. (F,W,S)
Chem 6BL. Introductory Inorganic Chemistry Laboratory (3)
Introduction to experimental procedures used in synthetic, analytical, and physical chemistry. If 6BL is a requirement for your major, it should be taken concurrently with 6B, or 6C. A materials fee is required for this course.(F,W,S)
Chem 6C. General Chemistry (4)
Third quarter of a three-quarter sequence intended for science and engineering majors. Topics include: electrochemistry, kinetics, coordination chemistry, nuclear chemistry, and an introduction to organic and biochemistry. Three hours' lecture, one hour recitation. Prerequisite: Chem. 6B; Chem. 6BL may be taken concurrently. A materials fee is required for this course. (F,W,S)
Chem 112B. (Molecular Biochemistry Laboratory) (6) or BIMM 101 (Recombinant DNA Lab) (4)
Chem 112B. Molecular Biochemistry Laboratory (6)
This laboratory will introduce the students to the tools of molecular biology and will involve experiments with recombinant DNA techniques. Prerequisites: Chem. 114A-B, Chem. 114C (may be taken concurrently); Chem. 143A and 143B. (Note: Students may not receive credit for both Chem. 112B and BIMM 101.) (S)
Chem 114B. Biochemical Energetics and Metabolism (4) or BIBC 102 (Structural & Metabolic Biochemistry (4)
Chem 114B. Biochemical Energetics and Metabolism (4)
This course is an introduction to the metabolic reactions in the cell which produce and utilize energy. The course material will include energy-producing pathways: glycolysis, Krebs cycle, oxidative phosphorylation, fatty-acid oxidation. Biosynthesis-amino acids, lipids, carbohydrates, purines, pyrimidines, proteins, nucleic acids. Prerequisite: Chem. 114A. (Note: Students may not receive credit for both Chem. 114B and BIBC 102) (W)
Chem 114D: Molecular and Cellular Biochemistry (4) or BIMM 100 (Molecular Biology) (4)
Chem 114D: Molecular and Cellular Biochemistry (4)
This course represents a continuation of 114C, or an introductory course for first- and second-year graduatestudents, and covers topics in molecular and cellular biochemistry. Emphasis will be placed on contemporary approaches to the isolation and characterization of mammalian genes and proteins, and molecular genetic approaches to understanding eukaryotic development and human disease. Prerequisites: Chem 114 A-C or consent of instructor. (May not be offered every year.)
Chem 127. Physical Chemistry (4) or BIBC 110. Physical Biochemistry (4
Chem 127. Physical Chemistry (4)
An introduction to physical chemistry with emphasis on biochemical and environmental applications.Thermodynamics, first and second laws, thermochemistry, chemical equilibrium, solutions, kinetic theory reaction kinetics. Prerequisite: Chem. 126 or consent of instructor. (W)
Chem 140A. Organic Chemistry (4)
An introduction to organic chemistry, with emphasis on material fundamental to biochemistry. Topics include bonding theory, isomerism, stereochemistry, chemical and physical properties, and an introduction to substitution, addition, and elimination reactions. Prerequisite: Chem. 6C or equivalent course in general chemistry.(Note: Students may not receive credit for both 140A and 141A.) (F,W,S)
Chem 140B. Organic Chemistry (4)
A continuation of 140A; acid/base reactions, chemistry of the carbonyl group, sugars, peptides, nucleic acids and other natural products. Prerequisite: Chem. 140A (a grade of C or higher in Chem. 140A is strongly recommended). (Note: Students may not receive credit for both 140B and 141B.) (F,W,S)
Mathematics Courses
Math 20A. Calculus for Science and Engineering (4) Foundations of differential and integral calculus of one variable. Functions, graphs, continuity, limits, derivative, tangent line. Applications with algebraic, exponential, logarithmic, and trigonometric functions. Introduction to the integral. (Two credits given if taken after Math. 1A/10A and no credit given if taken after Math. 1B/10B or Math. 1C/10C. Formerly numbered Math. 2A.) Prerequisite: qualifying score on placement examination or completion of Math. 4C with a grade of B or better.
Math 20B. Calculus for Science and Engineering (4) Integral calculus of one variable and its applications, with exponential, logarithmic, hyperbolic, and trigonometric functions. Methods of integration. Polar coordinates in the plane. (Two units of credits given if taken after Math. 1B/10B or Math. 1C/10C.) Prerequisite: Math. 20A or equivalent / Score of 4 or better on AB calculus AP test.
Math 21C. Calculus and Analytic Geometry for Science and Engineering (4)
Vector geometry, vector functions and their derivatives. Partial differentiation. Maxima and minima. Double integration. (Two units of credits given if taken after Math. 1C/10C. Formerly numbered Math. 2C.) Prerequisite: Math. 2B/20B or equivalent or consent of instructor.
Math 20F. Linear Algebra (4)
Matrix algebra, solution of systems of linear equations by Gaussian elimination, determinants. Linear and affine subspaces, bases of Euclidean spaces. Eigenval-ues and eigenvectors, quadratic forms, orthogonal matrices, diagonalization of symmetric matrices. Applications. Computing symbolic and graphical solutions using Matlab (Zero units given if Math. 2EA previously. Formerly numbered 2EA.) Prerequisite: Math. 21C (or 20C) or equivalent or consent of instructor.
Physics Courses
Phys 2A. Physics–Mechanics (4)
A calculus-based science-engineering general physics course covering vectors, motion in one and two dimensions, Newton's first and second laws, work and energy, conservation of energy, linear momentum, collisions, rotational kinematics, rotational dynamics, equilibrium of rigid bodies, oscillations, gravitation. Prerequisites: Mathematics 20A, and concurrent enrollment in Mathematics 20B. (F,W,S)
Phys 2B. Physics–Electricity and Magnetism (4)
Continuation of Physics 2A covering charge and matter, the electric field, Gauss's law, electric potential, capacitors and dielectrics, current and resistance, electromotive force and circuits, the magnetic field, Ampere's law, Faraday's law, inductance, electromagnetic oscillations, alternating currents and Maxwell's equations. Prerequisites: Physics 2A, Mathematics 20B, and concurrent enrollment in Mathematics 21C. (F,W,S)
Phys 2C. Physics–Fluids, Waves, Thermodynamics, and Optics (4)
Continuation of Physics 2B covering fluid mechanics, waves in elastic media, sound waves, temperature, heat and the first law of thermodynamics, kinetic theory of gases, entropy and the second law of thermodynamics, Maxwell's equations, electromagnetic waves, geometric optics, interference and diffraction. Prerequisites: Physics 2B, Mathematics 21C, and concurrent enrollment in Mathematics 21D. (F,W,S)
