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Winter Course Offerings

Winter 2017 Schedule

The winter semester is comprised of one 16 week term, and two 8 week terms. Standard full time status requires at least two courses per semester. The Halmos College of Natural Sciences and Oceanography program office reserves the right to cancel a course due to low registration. If canceled the students will have a choice of switching to a different course or receiving a full refund.

Course Schedule

Capstone, Thesis, Ph.D. Directed Study, Dissertation

M.S. students wishing to register for Capstone or Thesis Credits must have had their proposal accepted by the Oceanographic Campus Program Office. A student who has not had their proposal approved by the program office may have to register for a Directed Independent Study and must contact the Program Office ( for the Course Reference Number (CRN) associated with their major advisor.

Once a proposal has been approved by the Chair of the Department, MS students sequentially register for and complete credits in each succeeding semester until the capstone/thesis is complete and has been successfully defended.  If a student fails to register for any given term without written approval by the Chair of the Department, that student will be withdrawn from the program.

Ph.D. students register for directed study credits if their proposal has not been approved.

To select the correct CRN, please choose your major and track.  Then select your major advisor.

Capstone, Thesis, Ph.D. Directed Study, Dissertation Schedule

Course Descriptions

Learn more about each course below.

Core Courses:

MSMS 5010 Biostatistics:

This graduate course will introduce the most commonly used statistical tests and procedures to analyze biological and ecological data. The main objective is to prepare the students to identify the most correct statistics to analyze biological data, perform the statistical analysis in R and correctly interpret the results. Lectures will consist of short theoretical presentations followed by a lab where students will do guided exercises in R. Students will be required to do readings prior to the class on the theoretical basis of the theme of the week, and perform unguided exercises (homework) to cement knowledge.

MSMS 5020 Marine Ecosystems:

This class focuses on marine ecological processes and functions. It presents an overview of the basic concepts of marine ecology along with more detailed elements of the discipline including the diversity of marine ecosystems, trophic relationships, ecological roles, and nutrient cycling and biogeochemistry.

MSMS 5030 Marine Geology:

Marine Geology reviews key concepts of marine geology, as needed by marine biologists to understand the geomorphic setting they are working in and to provide a general-knowledge background. Since it is graduate-level, students are required to enhance frontal classroom teaching by the instructor through research papers and their presentation on specialized subjects directly related to the taught material. Course material reviews planetary evolution, types of sediments and rocks, the reason for the existence of oceans and continents and the spatio-temporal dynamics of marine sedimentary and igneous processes. Numerous case studies are used to illustrate concepts such a plate tectonics via island formation, and sedimentology via discussion of attractive sedimentary systems, such as coral reefs. Students will have a broad understanding of geological ocean dynamics and will be literate in present issues in the Earth Sciences.

Furthermore, since quantitative data analysis is a key skill required on the job-market, students will be introduced to the freeware statistical software R and will be exposed to the analysis of realistic geological datasets.

MSMS 5040 Marine Chemistry:

This course is an introduction to marine chemistry. It describes the properties, composition, and origin of seawater; the importance, distribution, relationships, and biogeochemical cycling of the major inorganic nutrients, dissolved gases, trace metals, and organic compounds. Salinity, temperature and density distributions will be explained. Carbonate parameters (pH, Alkalinity, TCO2 and pCO2) and how these are influenced by uptake of anthropogenic carbon dioxide by the ocean will be a key topic. Material is presented through lectures and three laboratory sessions which cover the principles and application of selected analytical techniques.

MSMS 5050 Physical Oceanography:

This course is intended to give students a view to how wind, radiation, gravity, friction, and the Earth's rotation determine the ocean's temperature and salinity patterns and currents. Some important process we will study include heat budget of the oceans, exchange of heat with the atmosphere and the role of the ocean in climate, surface mixed layer, waves in the ocean, geostrophy, Ekman transport, upwelling, Rossby waves, subtropical gyres, western and eastern boundary currents. Students will learn how to explain physical features of the ocean ranging from microscopic turbulence to global circulation.

MSMS 5060 Scientific Communication:

This professional development class is designed to broaden the graduate student’s career prospective and develop competencies in communication (written and oral), leadership/management abilities, and skills related to job acquisition.  This class will benefit students at any stage of their graduate career or pursuing any degree type (capstone, thesis, and dissertation).  


MSMS 6001 Marine Physiology:

This course examines various aspects of the functional biology of marine animals, including physiology, feeding, locomotion, morphology and sensory biology.  Basic functional biology and physiological concepts will be taught, and then expanded upon to identify how animals have adapted to deal with major biological challenges found in the marine environment, such as pressure and temperature extremes, large salinity fluctuations, extremely low light levels, etc.

MSMS 6004 Marine Fisheries:

This course will explain the main theories and methods used in marine fisheries science, as well as providing a basic understanding of management in the United States (the federal fisheries management council system and international regional fisheries management organization processes).  Ultimately, the student will better understand the historical development of the structure and goals for U.S. domestic fisheries policies.  In addition, this course includes several laboratory exercises and guest lectures, including fishing gear modifications, fish specimen preparation, and basic population modeling.

MSMS 6008 Biology of Sharks and Rays II:

Although the study of sharks generally lags behind studies on bony fishes and many other animals, our understanding of the biology of sharks and rays has improved tremendously over the past several decades.  There is tremendous diversity within sharks and rays and this diversity reflects the evolutionary history and range of lifestyles of these animals.  A combination of heavy fishing pressure on shark populations and their general vulnerability to overexploitation has led to serous declines in shark populations throughout the world.    We will survey the evolution and diversity of past and present sharks and rays and also examine distributions, environments inhabited, ecological roles, interactions within and among species, and review the life history characteristics of sharks and rays in relation to their occurrence and sustainability in fisheries with the overall goal of understanding the diversity of sharks and rays, their role in marine ecosystems and their interactions with humans (other than in terms of shark attack).  

MSMS 6015 Fertilization Ecology:

This course gives a general overview of fertilization ecology focusing in marine free-spawning invertebrates and fish. Students will discover the many obstacles to reproductive success in free-spawning marine organisms (i.e., distance, dilution, timing, egg location, species specificity, competition, prevention of polyspermy) and the potential benefits of this reproductive strategy. Topics covered in this course include: sperm chemotaxis, gamete recognition proteins, sperm competition, sperm motility, polyspermy, Allee Effect, gamete aging, fertilization models and the effect of hydrodynamics on fertilization. This course will consist of lecture, discussions, and laboratory experiments.

MSMS 6016 Ichthyology:

This course will provide a thorough coverage of ichthyology, the study of fishes. The focus will be on the systematics of bony, cartilaginous and jawless fishes, both living and extinct. The anatomy of fishes will be detailed, followed by a multi-lecture series treating the major lineages of fishes. Lab exercises will involve anatomical study and taxonomy of extant fishes. Following systematic lectures key ecological aspects of fishes will be examined, including trophic ecology, growth and reproduction, and community structure. These ecological elements will be traced back to the evolution of major lineages to allow student understanding of why certain fish groups occur (or do not occur) where they do. In addition to in-lab work, students will gain experience in field sampling techniques around the Oceanographic Center in order to acquire fresh material for laboratory exercises.

MSMS 6021 Histology & Ultrastructure of Marine Organisms:

This intensive course will examine the fine and ultrastructure of marine organisms and range in focus from bacterial cells to fish tissue. Lectures and labs will be conducted to examine structure and function of tissue and cells of several marine groups. Light and electron microscopy in conjunction with molecular methods for study of bacterial cells such as FISH (Fluorescence In-situ hybridization) will be discussed. Additionally, the complementary nature of cell and tissue imaging using light and electron microscopy will be examined.  Fixed and embedded blocks of student research specimens will be supplied and students will section and stain their samples for examination in the light and/or electron microscope. Imaging and image capture methods including quantification of structural features using ImageJ will be conducted. Students will prepare their results for presentation and submit a term paper at the end of the semester. 

MSMS 6204 Anthropogenic Impacts in Marine Environments:

Humankind has always tended to settle around the coastal zone, and the world's oceans have long been a source of transport and natural resources, from fisheries to minerals. However, the oceans and their currents are giant interconnected conveyors of all nations’ anthropogenic marine impacts. This course will focus upon the historical patterns and influences associated with anthropogenic activities in the marine and coastal environment as well as examining anthropogenic marine impacts with policies, critical resource limitations and related slowing global economic growth. To do so, the course will examine present day major anthropogenic marine impacts, mitigation efforts, and the economic trends and future trajectories associated with human development, critical resource limitation, and related impacts on the marine environment while considering the resulting net economics resources for forecasting, ameliorating and mitigating them.

MSMS 6205 Toxicology and Laboratory q-PCR:

The first week of the course will be training in the classical culture techniques for determination of fecal pollution in surface waters as is used in all water quality laboratories. This will involve membrane filtration for bacterial indicators and plaque formation for viral indicators.

During the second week newly developed real time PCR methods will be performed and evaluated. The use of q-PCR has been implemented in microbiology studies to quantify abundance and expression of taxonomic and functional gene markers that pose contamination threats to drinking, recreational, marine, and fresh waters. Its use allows viable results for the indication of microbial presence associated with human pollution that supersedes the abilities of culture based fecal coliform and enterococci studies. The use of PCR chemistries is a more advanced, precise and sensitive method for estimating microbial species in environments. Within PCR chemistries, q-PCR allows for expedient results coupled with greater accuracy to determine if human pollution is contaminating a water source and in what amounts quantitatively.

MSMS 6208 Aquaculture:

This course will give the student an understanding of the basic principles of aquaculture, including production systems, water quality, nutrition, spawning, larval culture and grow-out, and culture methodologies of fish, reptiles, invertebrates (zooplankton, molluscs, crustaceans, corals) and algae. The course will consist on a series of lectures followed by readings for each learning topic and paper discussions. The students will have the opportunity to conduct hands-on activities associated with the culture and husbandry of animals.

MSMS 6210 Scientific Method and Experimental Design:


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