Graduate Course Listings

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Graduate Courses for Agricultural and Biological Engineering

ABE 5015: Empirical Models of Crop Growth & Yield Response

Semester Taught: Spring

Credits: 3

ABE5038: Fundamentals and Applications of Biosensors
The course is intended to provide a broad introduction to the field of biosensors, design and performance analysis. Fundamental application of biosensor theory will be demonstrated, including recognition, transduction, signal acquisition, and post processing/data analysis.

Prereq: Senior standing required. Passing grad in organic chemistry (CHE 2210/2211, EES 4200, or equivalent) and differential equations (MAP 2302 or equivalent) is required. Recommended background in basic biology.

The topics of the interdisciplinary course take into consideration that students will be coming to the class from varied backgrounds. Proper background materials will be provided when needed. It is, however, the student's responsibility to see the instructor if he/she does not have sufficient background in a particular topic. In this case additional background materials and discussion can be provided or directed as needed.

Semester Taught: Spring

Credits: 3

ABE 5152: Electro-Hydraulic Circuits and Control
Engineering analysis, design and experimentation of electro-hydraulic circuits and systems. Including the design of hydraulic circuits, fluid power system components, hydraulic actuator analysis, servo and proportional valve performance, and elecro-hydraulic control theory and applications.

Prereq: Fluid dynamics or permission of instructor

Semester Taught: Spring

Credits: 3

ABE 5332: Advanced Agricultural Structures
Design criteria and analysis techniques for agricultural structures including structural and analysis, thermal analysis, air and moisture relationships (psychometrics), environmental modification and control, and plant and animal environmental physiology.

Semester Taught: Fall

Credits: 3

ABE 5442: Bioprocess Engineering
The course will cover engineering principles, processes and techniques for using biological agents such as cells, enzymes or antibodies for the production of chemicals, food, biofuels and pharmaceuticals, and waste treatment. The course will include stoichiometry and kinetics of reactions that employ biological agents; design, analysis and operation of reactors (fermenters); and product recovery and purification (downstream processing).

Prereq: Life Sciences, Biological, Chemical or Environmental Engineering coursework

Semester Taught: Fall

Credits: 3

ABE 5643C: Biological Systems Simulation
Introduction to concepts and methods of process-based modeling of biological systems; physiological, populational, and agricultural applications.

Prereq: MAC 2312. This course assumes no modeling experience or computer programming. Familiarity with differential equations can aid in most sections of the course.

Semester Taught: Fall

Credits: 3

ABE 5646C: Agricultural and Biological Systems Simulation
Basic concepts of systems analysis, modeling, and computer simulation of dynamic biological and agricultural systems. Methods for working with models, including sensitivity analysis, parameter estimation, and model evaluation. Applications of models in agricultural and biological systems.

Prereq: MAC 2312, CGS 3460 or CIS 3020

Semester Taught: Spring

Credits: 3

ABE 5653C: Physical and Rheological Properties of Biological Materials
Theory and use of physical and rheological properties of biological materials in agricultural and biological engineering applications

Prereq: CHM 2045, MAC 2313 and PHY 2048

Semester Taught: Spring

Credits: 3

ABE 5663: Applied Microbial Biotechnology
The course will focus on quantification of microbial growth and microbially mediated degradation and transformation processes emphasizing the application of these tools to develop mathematical models for industrial processes for pollution control, waste treatment, biofuel and bioproducts production and bioremediation.

Prereq: Bioprocess Engineering

Semester Taught: Spring

Credits: 3

ABE 5707C: Agricultural Waste Management
Engineering analysis and design of systems for the collection, storage, treatment, transport, and utilization of disposable organic wastes and wastewaters. Field trips to operating systems and laboratory evaluation of materials and processes.

Prereq: $ or higher classification

Semester Taught: Fall

Credits: 3

ABE 5815C: Food and Bioprocess Engineering Unit Operations
Design and analysis of thermal, freezing, evaporation, dehydration; and mechanical, chemical and phase separations processes as governed by reaction kinetics and rheology of food and biological materials.

Prereq: ABE 3612, EML 3100, and CWR 3201

Semester Taught: Fall

Credits: 4

ABE 5936: Writing Grant Proposals for Scholarships and Fellowships
The course is intended to provide incoming graduate students in the Agricultural and Biological Engineering Department a broad introduction to opportunities for obtaining scholarships, fellowships, internships, and teaching/research assistantships from federal funding agencies. The course will introduce the students to funding sources and opportunities, provide guidelines for proposal writing, and require students to prepare a mock proposal which will be reviewed by the instructor and students enrolled in the course.

Prereq: Must be enrolled in the Agricultural and Biological Engineering graduate program. If the student has not taken a technical writing elective, they must contact the instructor to be eligible to register for the course.

Semester Taught: Fall

Credits: 2

ABE 6005: Applied Control for Automation and Robotics
Introduction to industrial controls, programmable logic controllers, and manipulator application programming in agricultural and biological engineering. Kinematics, dynamics and control strategies for serial link manipulators in agricultural applications.

Prereq: EML 5311, equivalent, or consent

Semester Taught: Spring (Odd Years)

Credits: 3

ABE 6031: Instrumentation in Agricultural Engineering Research
Principles and application of measuring instruments and devices for obtaining experimental data in agricultural engineering research.

Semester Taught: Fall

Credits: 3

ABE 6035: Advanced Remote Sensing in Engineering: Science and Sensors
To develop an understanding of remote sensing theory and systems in visible; near-, mid-, and thermal-infrared; and microwave regions of the EM spectrum.

Prereq: Differential and Integral Calculus

Semester Taught: Spring

Credits: 3

ABE 6037C: Remote Sensing in Hydrology
To develop a practical understanding of remote sensing applications to hydrology using observations in different regions of the EM spectrum.

Prereq: ABE 4036 or ABE 6035

Semester Taught: Fall (Even Years)

Credits: 3

ABE 6252: Advanced Soil and Water Management Engineering
Physical and mathematical analysis of problems in infiltration, drainage, and groundwater hydraulics.

Semester Taught: Spring (Even Years)

Credits: 3

ABE 6254: Simulation of Agricultural Watershed Systems
Characterization and simulation of agricultural watershed systems including land and channel phase hydrologic processes and pollutant transport processes. Investigation of the structure and capabilities of current agricultural watershed computer models.

Prereq: Working knowledge of hydrology and high-level programming language (Fortran, VBasic, C/C++, java, or environments like Matlab, Mathematica, COMSOL, etc.).

Semester Taught: Fall (Odd Years)

Credits: 3

ABE 6265: Vadose Zone Water and Solute Transport Modeling
Unsaturated zone modeling of water flow and solute transport processes. Comparative analysis of alternative mechanistic modeling approaches of different complexity.

Prereq: Requires computer literacy and a background on, or willingness to learn, a high-level computer language (i.e. Fortran C, Java, Visual Basic, etc.) or numerical computing environment (i.e. Matlab, Mathematica, etc.)

Semester Taught: Summer A (Even Years)

Credits: 3

ABE 6266: Nanotechnology in Water Research
Applications of environmental nanotechnology to water quality control. Fate and transport of nanomaterials in hydrologic pathways

Prereq: Basic knowledge of hydrology, environmental engineering, and water chemistry

Semester Taught: Fall

Credits: 3

ABE 6615: Advanced Heat and Mass Transfer in Biological Systems
Analytical and numerical technique solutions to problems of heat and mass transfer in biological systems. Emphasis on nonhomogeneous, irregularly-shaoed products with respiration and transpiration.

Prereq: CGS 3422 and AGE 3612C

Semester Taught: Spring (Even Years)

Credits: 3

ABE 6645C: Computer Simulation of Crop Growth and Management Responses
This course will teach the scientific background of comprehensive computer models for the dynamic simulation of crop growth, development, and yield, and soil and plant water, nutrient, and carbon dynamics, and the application of crop models to real-world problems. It will be based on a systems analysis approach.

Recommended that students have a basic understanding of crop and soil science

Semester Taught: Summer C

Credits: 3

ABE 6654C: Advanced Biobased Products From Renewable Resources
This course is intended to provide the knowledge for the production of energy (fuels), chemicals and materials from renewable resources. The course includes the fundamental principles and practical applications from renewable materials to bio-based materials: biorefinery and biobased products overview, fundamental concepts in understanding biorefinery and biobased products; biomass production; materials from biomass; chemical platforms from biomass; energy and fuels from biomass; pilot-plant and process design.

Prereq: Recommended knowledge in general chemistry. The topics of this interdisciplinary course take into consideration that students will be coming to the class from varied backgrounds. Proper background materials will be provided when needed.

Semester Taught: Fall

Credits: 3

ABE 6905: Individual Work in Agricultural & Biological Engineering

Credits: 1-4 (Max 6)

ABE 6931: Seminar

Credits: 1 (max 2)

ABE 6933: Applied Case Study Data Analysis

Semester Taught: Spring

Credits: 3

ABE 6933: Data Diagnostics: Detecting and Characterizing Deterministic Structure in Time Series Data
Application of nonlinear time series analysis to detect, characterize, and model deterministic structure in real-world time series data. Topics include signal processing, phase space reconstruction, surrogate data testing, causal network analysis, and phenomenological modeling.

Semester Taught: Fall

Credits: 3

ABE6933: Foundations of Probability and Math Statistics
This course is a fast-paced introduction to calculus-based probability and statistics aimed at graduate students in engineering and quantitative life sciences. It covers the essentials of STA5325 and STA5328 in a single semester making use of calculus and basic scientific computing to gain understanding about fundamental results and methods of probability and statistics.

Knowledge of calculus of multiple variables. Experience reading and writing simple computer programs in a scripting language (ideally, in R); basic knowledge of scientific computing (e.g., ABE 5643C for ABE students). Undergraduate statistics or a recent first graduate statistical methods class (such as ALS5932 or STA6166) is preferred.

Semester Taught: Spring

Credits: 3

ABE 6933: Logistics of Agricultural Food Chains
This course covers logistic strategy and concepts for agricultural food chains, and the techniques and tools needed to improve supply chain efficiency and solve logistics problems.

Prereq: Basic skill of Math and Statistics, knowledge of farming operations

Semester Taught: Spring

Credits: 3

ABE 6933: Seminar on Stochastic Modeling in Ecology and Hydrology
This course takes a problem-based approach to introduce stochastic modeling in context of ecology and hydrology. The students will be asked to study selected papers in detail, through reading and in-class discussion, such that they understand how to set up the problems and derive some results and mathematical expressions reported therein.

Prereq: Graduate standing. Basic calculus and college-level probability course.

Semester Taught: Fall

Credits: 3

ABE6933: Statistical Machine Learning
This course focuses on methodology and application of tools of statistical (machine) learning. In contrast with courses with similar names offered by Computer Science (CS) and Industrial Engineering (IE), it emphasizes statistical approaches to machine learning. The course prioritizes application and the intuition behind statistical methods rather than formal derivations and justification of the procedures.

Prereq: Recent first graduate statistical methods class (such as ALS5932 or STA6166). Experience reading and writing simple computer programs in a scripting language (ideally, in R). Basic undergraduate quantitative training (calculus and basic matrix/linear algebra). Stats/biostats grad students with stronger math and stats background are welcome.

Semester Taught: Fall

Credits: 3

ABE 6933: Modeling Coupled Natural-Human Systems
In this course, we will explore some approaches to modeling coupled natural-human systems (CNHs). By definition, modeling such systems requires concepts drawn from both natural and social sciences, a selected few of which will be studied in this course.

Prereq: Basic calculus and college-level probability courses

Semester Taught: Spring

Credits: 3

ABE6933: Fundamentals & Applications of Solar Energy

Semester Taught: Spring

Credits: 3

ABE 6933: Spatial Statistics
This course is an introduction to spatial statistics, with a focus on methods that are relevant for public health applications, as well as earth and environmental sciences. It is primarily intended for two audiences: (i) statisticians who want to get exposed to methods and applications and (ii) researchers from other elds with some training in statistics that routinely work with spatial data and would like to learn appropriate statistical models and methods.

Sufficient background: First-year required masters-level coursework in statistics at UF.

Minimal sufficient background: a solid graduate course in regression (such as STA6207) with exposure to matrix notation; a solid course in inference at the level of STA5328; basic scientific and statistical computing skills; motivation (particularly, to pick up R)

Ideal background: in addition to the minimum background above, proficiency with matrix algebra and basic numerical linear algebra (STA6329); statistical computing using R; exposure to linear mixed models, generalized linear models and generalized linear mixed models; masters level sequence in probability and inference STA 6326-6327; interest (and/or need) to apply methods learned in this course in your research work.

Semester Taught: Fall

Credits: 3

ABE 6940: Supervised Teaching

Credits: 1-5 (Max 5)

ABE 6971: Research for Master's Thesis

Credits: 1-15

ABE 6974: Non-Thesis Project

Credits: 1-15

ABE 6986: Applied Mathematics in Agriculture & Life Sciences
Mathematical methods, including regression analysis, graphical techniques, and analytical and numerical solution of ordinary and partial differential equations, relevant to engineering in agriculture and the related sciences.

Prereq: MAP2302 or equivalent

Semester Taught: Spring

Credits: 3

ABE 7979: Advanced Research

Credits: 1-12

ABE 7980: Research for Doctoral Dissertation

Credits: 1-15

AGG5607: Communicating in Academia - Guide for Graduate Students
This course is designed to teach graduate students about academic writing, specifically focused on research proposals, theses, dissertations, manuscripts, grant proposals, and CVs. The course was developed to teach students about aspects of academic writing that are not normally part of graduate curriculum but are necessary to succeed.

Semester Taught: Spring (Online)

Credits: 3

CWR 6536: Stochastic Subsurface Hydrology
Stochastic modeling of subsurface flow and transport modeling including geostatisitcs, time series analysis, Kalman filtering, and physically based stochastic models.

Prereq: Calculus (through ordinary differential equations), undergraduate probability and statistics, and previous coursework in subsurface hydrology. Familiarity with computer operating systems and computer programming will be assumed.

Semester Taught: Fall (Even Years)

Credits: 3

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Graduate Courses for Agricultural Operations Management

AOM 5334C: Agricultural Chemical Application Technology
Equipment and methods used to apply pesticides in agriculture. Emphasis on techniques to avoid misapplication and pesticide drift.

Semester Taught: Fall

Credits: 3

AOM 5435: Advanced Precision Agriculture
Principles and applications of technologies supporting precision farming and natural resource data management planning. Global positioning system (GPS), geographic information system (GIS), variable rate technologies (VRT), data layering of independent variables, field sensors and computer software for precision farming.

Prereq: Graduate student standing or permission of instructor

Semester Taught: Fall (Even Years)

Credits: 3

AOM 6735: Irrigation Principles and Management
This course is designed to teach graduate students about irrigation such that they would have the skills to evaluate an irrigation system, identify parts of a system, and develop an irrigation schedule based on system characteristics. This course is designed for non-engineers although quantitative ability will be required for calculations and analysis.

Prereq: Students must be proficient in Microsoft Excel and Word. Students should be able to use equation functions and graphing functions in Excel. It is recommended that students have basic understanding of hydrology, unit conversions, and algebra. 

Semester Taught: Fall (Online)

Credits: 3

AOM 6932: Principles and Issues in Environmental Hydrology
This is a basic course in Environmental Hydrology intended for Agricultural and Natural Resource Managers. The first half of the course covers scientific principles of the hydrologic cycle while, the second half investigates case studies of current water quality and water management issues.

Prereq: This course will use simple and intermediate algebraic equations and trigonometry. Sophomore level chemistry and physics as well as mathematics through pre-calculus are recommended. Significant experience with Microsoft Excel or similar spreadsheets is required in select assignments.

Semester Taught: Fall (Online)

Credits: 3

AOM 6932: Agri-Food Systems Innovation
This course is open to undergraduates and graduates alike and requires students to explore the role of innovation in food systems from a reverse chain perspective. Students will gain knowledge of the food system framework from a multi-level (i.e., global, national, and regional/local) perspective, identify current, innovative business and technological practices, as well as present and think critically about future trends in food.

Semester Taught: Spring

Credits: 3

AOM 6905: Individual Work in Agricultural Operations Management

Credits: 1-6 (Max 6)

AOM 6932: Sustainable Agricultural Intensification

Semester Taught: Spring

Credits: 2

AOM 6932: Special Topics in Agricultural Operations Management

Credits1-6 (Max 6)

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Graduate Courses for Packaging

PKG 5003: Advanced Distribution & Transport Packaging
Topics related to the technical aspects of a systems approach to designing packaging for shipping in order to provide product protection and to facilitate safe and cost-effective distribution. Will include an overview of the distribution system environment, transportation types and testing procedures, as well as tracking technologies for packages. Each team will prepare and execute a protective shipping container that will be tested in real conditions. The rating and the performance will be evaluated in part by experts working in the industry.

Semester Taught: Spring

Credits: 3

PKG 5006: Advanced Principles of Packaging
Presents materials, uses, functions and production processes of packaging. Topics will include an industry overview of packaging and related applications. The historical, societal and technological drivers of packaging will be discussed. Examples will include how an end-user of packaging decides on the product/package combination they use and the impact these choices make on the market success of a product.

Semester Taught: Fall

Credits: 3

PKG 5105: Advanced Consumer Products Packaging

Semester Taught: Spring

Credits: 3

PKG 6100: Advanced Computer Tools for Packaging
Covers powerful computer tools applicable to the packaging industry. Topics include label design, bar code technology, spreadsheet programming, 3D package design and distribution efficiency analysis.

Semester Taught: Fall

Credits: 3

PKG 6905: Individual Work in Packaging

Credits: 1-6 (Max 6)

PKG 6932: Special Topics in Packaging Science

Credits: 1-6 (Max 6)

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