Computational Biology Program Course Descriptions
COP 3014. Programming I (3). Prerequisite: MAC 1140. Fundamental concepts and skills of programming in a high-level language. Flow of control: sequence, selection, iteration, subprograms. Data structures: arrays, strings, structs, ADT lists and tables. Algorithms using selection and iteration (decision making, finding maxima and minima, basic searching and sorting, simulation, etc.). Good program design using a procedural paradigm, structure and style are emphasized. Interactive and file IO. Testing and debugging techniques. Intended primarily for Computer Science or Computer Engineering majors, or anyone who is required to take COP 3330.
COP 3344. Introduction to UNIX (1). This is an introductory course in the use of the UNIX operating system designed for both majors and non-majors. This course will introduce students to the UNIX computing environment at Florida State University, Department of Computer Science. Topics will include: UNIX history, requesting UNIX accounts, logging in to a UNIX system, basic operating system concepts and file structure, basic commands, text editor(s) (to include emacs, vi, and pico), printing, mail, and online help. The goals of this course are to enable students to Login to their UNIX account from any type of computer and have a basic understanding of the commands and utilities.
COP 3330. Object Oriented Programming (3). Prerequisite: COP 3014. Pre- or Corequisite: COP 3344. Object-oriented programming in a modern programming language; classes, objects, inheritance, and polymorphism; introduction to data structures and container classes.
CDA 3100. Computer Organization I (3). Prerequisites: COP 3330, MAD 2104. This is a core course intended for computer science majors with previous C/C++ Language background. The course introduces fundamental concepts in computer organization and digital logic design, including numbering systems and number representation, logic gates and design, the Von-Neumann architecture principle, and the machine instruction cycle. Assembly language programming with C language interfacing is also presented, reinforcing basic computer structure and machine cycle operation principles.
COP 4530. Data Structures, Algorithms and Generic Programming (3). Prerequisites: COP 3330, MAD 2104. Pre- or Corequisite: CDA 3100. Definition, use and implementation of generic data structures using a modern programming language; reusable program components.
CDA 3101. Computer Organization II (3). Prerequisite: CDA 3100. Fundamental concepts in processor design, including datapath and control, pipelining, memory hierarchies, and I/O.
COP 4531. Complexity and Analysis of Data Structures and Algorithms (3). Prerequisites: COP 4530, MAD 3105, STA 4442. Analysis of the complexity of algorithms, including sorting, searching, and graph algorithms; use and implementation of graphs.
COP 4710. Theory and Structure of Databases (3). Prerequisites: COP 3330, MAD 2104. Theory of relational and object-oriented databases; relational database management systems and SQL; design, development, and implementation issues in database systems.
COT 4420. Theory of Computation (3). Prerequisite: MAD 3105. Introduction to the theory of computation, including models of computation such as Turing machines; theory of programming languages, including grammars, parsing, syntax and semantics.
BSC 2010. Biological Science I (3). Corequisites or prerequisites: BSC 2010L; CHM 1045C. Basic chemistry, energetics, metabolism, and cellular organization; molecular genetics and information flow; animal and plant function.
BSC 2011. Biological Science II (3). Prerequisites: BSC 2010/2010L. Reproduction and development, transmission (Mendelian) genetics, population biology, ecology, and evolution.
PCB 3063. General Genetics (3). Prerequisites: BSC 2011/2011L; CHM 1046C. Introduction to the principles of transmission and molecular genetics of procaryotes and eucaryotes and significance of these principles to other aspects of biological science.
PCB 4674. Evolution (3). Prerequisites: BSC 2011/2011L; CHM 1046C; PCB 3063; senior standing (90+ hrs.) Emphasis on the processes of evolution: origin of life, theories of evolution, sources of variation, natural selection, population systems, isolating mechanisms, evolution above the species level.
BOT 4394. Plant Molecular Biology (3). Prerequisites: BOT 3015; BSC 2010/2010L, 2011/2011L; CHM 1045C, 1046C. Pre- or Corequisite: PCB 3063. This course explores molecular biology and biotechnology of plant growth and development.
BSC 2010L. Biological Science I Laboratory (1). Corequisite or prerequisite: CHM 1045C. Corequisite: BSC 2010. This laboratory furnishes tools and techniques used to visualize, quantify, analyze biological phenomena, including experimental design and execution, recording of data, and graphic and statistical analysis of data.
BSC 2011L. Animal Diversity Laboratory (2). Prerequisites: BSC 2010/2010L. Introduction to animals, sponges, cnidarians, flatworms and pseudocoelomates, annelids, molluscs, arthropods, echinoderms, and chordates.
BSC 4613. Systematics (3). Prerequisites: BSC 2011/2011L; CHM 1046C. History of systematic theory; methods of phylogenetic analysis including distance, parsimony, and likelihood; classification of the diversity of life; the comparative method; analysis of within species variation.
MCB 4403. Prokaryotic Biology (3) Prerequisites: BSC 2011/2011L; CHM 1046C, 2210; PCB 3063. Corequisite: MCB 4403L. Structural and functional characteristics of microorganisms, with emphasis on prokaryotes (bacteria and archaea) and viruses. Topics include: prokaryotic cell structure and function, physiology and genetics of prokaryotes and viruses, physiological and molecular aspects of microorganisms and human disease, and biotechnological applications of microbial physiology (environmental, food, and industrial microbiology).
MCB 4403L. Prokaryotic Biology Laboratory (2). Prerequisites: BSC 2011/2011L; CHM 1046C, 2210; PCB 3063. Corequisite: MCB 4403. Laboratory methods for growth, handling, and study of prokaryotes and other types of microorganisms. Topics include: aseptic technique and isolation of pure cultures; microscopic methods; effects of environment on growth; viruses; physiological characterization methods; and methods related to medical, environmental, and food microbiology.
PCB 3134. Cell Structure and Function (3). Prerequisites: BSC 2011/2011L; CHM 1046C. Cellular chemistry and physiology, morphology, and function of cellular organelles; cellular motility, growth, division, communication, and regulation.
PCB 3743. Vertebrate Physiology (3). Prerequisites: BSC 2011/2011L; CHM 1046C. Physiological systems of vertebrates with emphasis on mammals. Mechanisms underlying physiological processes and the physico-chemical principles upon which they depend.
PCB 4024. Molecular Biology (3). Prerequisites: BSC 2011/2011L; CHM 1046C; PCB 3063; PCB 3134 recommended. The molecular basis of cellular function with emphasis on the activities of DNA, RNA, and the regulation of gene expression.
PCB 4233. Immunology (3). Prerequisites: BSC 2011/2011L; CHM 1046C; CHM 2210; PCB 3063, 3134, or permission of instructor. Analysis of the tissues, cells, and molecules of the immune system and their relationships to disease and transplantation.
PCB 4253. Animal Development (3). Prerequisites: BSC 2011/2011L; CHM 1046C; PCB 3063. Discusses a number of topics, including fertilization, early embryonic events, organogenesis, differentiation, morphogenesis, cytoplasmic localization, determination, and differential gene expression.
PCB 4843. Fundamentals of Neuroscience (3). Prerequisites: BSC 2011/2011L; CHM 1046C; PCB 3134, 3743, or 4723. This course will emphasize cellular and molecular approaches to neuroscience and brain function and will emphasize simple model systems including invertebrates.
BSC 4933. Introduction to Bioinformatics (3). Prerequisites: COP 4530, PCB 3063. Much of modern biology is devoted to understanding how information at the level of the gene codes for physical traits. Recent advances in gene sequencing technologies have made it possible to determine the DNA sequences for entire genomes. Bioinformatics is an emerging discipline that seeks to provide a quantitative framework for understanding how genomic sequence and its variation affects the phenotype. This course is targeted at two kinds of students: (1) biologists and biochemists seeking to improve quantitative skills that will facilitate interpretation of their data and (2) students from mathematics, computer science, and other quantitative disciplines interested in learning to apply their skills in computational biology. A laboratory component complementing the lecture material is designed to provide practical and marketable skills. Evaluation is based on exams, homework assignments, and a project.
CIS 4930r. Special Topics in Computer Science (3). Prerequisite: at least six (6) semester hours in computer science or software engineering at or above the 4000 level. May be repeated to a maximum of twelve (12) semester hours.
CIS 4930. Algorithms in Computational Biology (3).. Prerequisites: COP4530, PCB4674, STA2171. Introduction to algorithm design; dynamic programming; sequence alignment; divide and conquer techniques; greedy algorithms. Introduction to computational complexity(NP, NP-complete problems). Introduction to convex/nonconvex optimization; non-convex optimization methos; local search methods; genetic algorithms; ant colony optimizations; stochastic optimization; energy based optimization; simulated annealing.
MAC 2311. Calculus with Analytic Geometry I (4). Prerequisites: MAC 1147, or MAC 1140 and 1114; or appropriate score on a mathematics placement examination. Polynomial, trigonometric, exponential and logarithmic functions; first and second derivatives and their interpretations; definition and interpretation of the integral; differentiation rules; implicit differentiation; applications of the derivative; antiderivatives; fundamental theorem of calculus. This course must be taken for reduced credit by students with prior credit for some of the content.
MAC 2312. Calculus with Analytic Geometry II (4). Prerequisite: MAC 2311 or MAP 2483. or appropriate score on a mathematics placement examination. Techniques of integration; applications of integration; series and Taylor series; differential equations. This course must must be taken for reduced credit by students with prior credit for some of the content.
MAD 2104. Discrete Mathematics I (3). Prerequisite: MAC 1140. Credit is not also allowed for MGF 3301. Mathematical techniques of definition and proof, with application to discrete domains; formal logic; elementary combinatorics; digraphs and relations; graphs, trees, and multigraphs; applications.
STA 2171. Statistics for Biology (4). Prerequisite: MAC 2311. STA 2171 is for biology majors only. Other students must have approval from the Department of Statistics. Only two (2) semester hours of credit are given for STA 2171 if "C–" or better has been previously earned in STA 2023. No credit is given for STA 2171 if a "C–" or better has been previously earned in STA 2122 or 3032, or QMB 3200. This course provides an introduction to statistics emphasizing applications to biology. Topics include: Descriptive statistics, elementary probablity, the binomial and normal distributions, confidence intervals and hypothesis tests for means and proportions, correlation and regression, contingency tables and goodness-of-fit tests as well as analysis of variance.
PHY 2053C. College Physics A (4). Prerequisites: MAC 1140 and 1113 with grades of "C–" or better; or appropriate score on a mathematics placement examination. Corequisite: CHM 1045. An introduction to mechanics, heat, and waves for non-physical science majors. Examples from biology, geology and medicine are incorporated. First course in a two-semester sequence. Calculus not required. Two lectures, one recitation, and one laboratory each week. Students who have previously received credit for PHY 2048C may not register for PHY 2053C. (Must also register for PHY 2053L.)
PHY 2053L. College Physics A Laboratory (0).
PHY 2054C. College Physics B (4). Prerequisite: PHY 2053C or 2048C. An introduction to electromagnetism, light, and modern physics for non-physical science majors. Two lectures, one recitation, and one laboratory each week. Students who have previously received credit for PHY 2049C may not register for PHY 2054C. (Must also register for PHY 2054L.)
PHY 2054L. College Physics B Laboratory (0).
CHM 1045C. General Chemistry I (4). Prerequisite: MAC 1105 ("C–" or better.) Topics in this course include chemical symbols, formulas and equations; the states of matter; electronic structure and bonding; and introduction to chemical laboratory practice. Course consists of lectures, recitations, and laboratory (must sign up for CHM 1045L to select meeting time.)
CHM 1045L. General Chemistry I Laboratory (0). Laboratory, three (3) hours per week. Corequisite: CHM 1045C. Safety goggles and a scientific calculator are required for every class.
CHM 1046C. General Chemistry II (5). Prerequisites: CHM 1045C or 1050 and 1050L (All "C–" or better.) Topics include elementary thermodynamics; acids and bases; equilibrium; rates and mechanisms of chemical reactions; introduction to quantitative laboratory techniques; and semi-micro qualitative analysis of common cations. Course consists of lectures, recitations, and laboratory (must sign up for CHM 1046L to select meeting time.)
CHM 1046L. General Chemistry II Laboratory (0). Laboratory three (3) hours per week. Corequisite: CHM 1046C. Safety goggles and scientific calculator are required for every class.
