Monterey Bay Aquarium Research Institute
2013 MBARI Summer Internship Program

2013 Projects and Mentors:

Below is a list of some potential projects and mentors. This list will be updated, so please bookmark and check this page from time to time. Clearly identifying a specific research interest/area is an important part of your application and is essential in the application process. Please contact George Matsumoto if you have any questions. Links to the mentors' home pages have been provided (when available) so that you can learn more about the various mentors, please DO NOT contact the mentor directly.

Nancy Barr

Science and technology illustration: This position is ideal for an intern with experience in translating science and technology concepts into visual media. This is not likely to include illustrations of individual animals, but rather the creation of visuals to explain complex processes, systems, or concepts that are not easily photographed. The intern would likely work on several different projects during the summer, and possibly in different formats (3D illustrations, drawing, animation, information graphics). Applications should include a portfolio (hard copy or digital) in addition to the other required material.

Jim Barry

Rising carbon dioxide levels: Rising atmospheric carbon dioxide levels are causing significant changes in ocean conditions, including warming, ocean acidification, and deoxygenation. Although each of these environmental changes can have important effects on the growth, survival, and reproduction of marine organisms, our understanding of the consequences of exposure to simultaneous effects of these potential stressors is poor. We plan to involve an MBARI intern in our laboratory and field studies to evaluate the response of various marine animals to changes in temperature, oxygen, and pH. The intern will most likely work on laboratory studies concerning the effects of these stressors on very young abalone.

Jim Bellingham

Long-range autonomous underwater vehicle (LRAUV): The LRAUV is being used to observe the evolution of ocean processes over periods ranging from a week to a month. Two possible projects are envisioned:

  1. This intern project would use data from past LRAUV missions to develop probabilistic state estimation of the vehicle for detecting vehicle failures. Such capabilities are particularly important given the long run times of the vehicle, as numerous failures occur during a period of weeks or months. At present the typical response to a failure is to surface and contact shore operators for help. The goal would be to create a framework that would allow faults to be characterized so that appropriate responses could be selected by the vehicle without interrupting the mission.
  2. Sensing of marine organisms is a critical capability for the LRAUV. This intern project would explore new sensing approaches for detecting organisms, particularly small organisms. Options include analysis activities which develop approaches to more effectively use the existing suite of sensors, as well as exploratory activities which would test new sensors for inclusion in the LRAUV sensor suite.
  3. The Drew Gashler Memorial Internship - this is specifically for a Moss Landing Marine Laboratory graduate student and could apply to either of the two projects above. Please specify (in your cover letter) that you are applying for the Drew Gashler Internship.

All LRAUV projects would include operation experience with the vehicle.

Peter Brewer and Ed Peltzer

Ocean chemistry: As a summer intern in the Brewer lab you will join a team busily involved in exploring new ways to examine the chemistry of the ocean. We use laser Raman techniques in the deep sea to explore the chemistry of pore waters such as the methane and sulfide signals which change radically if a core is brought to the surface. We examine the changing CO2 chemistry of the ocean, and how the growth of CO2 and decline in O2 will lead to the creation of greatly expanded dead zones, and the many consequences of this. A summer intern will be engaged in a specific aspect of this based upon abilities and experience.

Francisco Chavez

Ocean biogeochemistry: The biology and chemistry of the ocean varies in relation to changes in climate and ocean circulation. As a summer intern in the Chavez lab you will be exposed to instruments and methods to measure the biological and chemical content and characteristics (phytoplankton, primary production, bio-optics, carbon dioxide, nutrients, pH, oxygen) of ocean waters and how it is influenced by ocean circulation and climate. A project that links the biological and chemical response of the upper ocean to climate variability by using new measurements and analysis of data previously collected will be developed.

Judith Connor

Educational materials: This project would contribute engaging materials (computer animations and possibly written activities) to be used on the web and in informal educational programs about ocean chemistry and climate change. Experience in creating animations that work across platforms, web authoring, and informal education would be valuable. Knowledge of animation programs and Dreamweaver would be helpful. Applications should include digital examples of previous work in addition to the other required material.

Patrick Gibson and Josh Plant

Investigations of estuarine dynamics with in situ instrumentation: The Chemical Sensors program at MBARI develops a range of instruments for analyzing nutrient concentrations of marine environments in situ. Elkhorn Slough, a coastal watershed adjacent to MBARI and directly connected to Monterey Bay, has long served as a test subject for new and established sensor technologies. As a summer intern, you will be able to employ novel instrumentation to study nutrient dynamics in Elkhorn Slough at high spatial and temporal scales and with high analytical precision. The project details are flexible, but should aim to decipher critical inputs, sinks, physical mechanisms and biogeochemical processes regulating nutrient dynamics in Elkhorn Slough. Applicants should have general knowledge of nutrient analyses and biogeochemistry, estuarine ecology, and spatial and temporal data analysis techniques.

Steve Haddock

Bioluminescence and jellies: Interns will select from a range of topics related to the biodiversity, bioluminescence, and fluorescence of gelatinous zooplankton. Depending on their specific interests, the project could involve molecular biology and sequence analysis, morphology, chemistry, processing of oceanographic data, or analysis of transcriptome data from a variety of deep-sea organisms. Successful applicants will show a special interest in one of these sub-topics, and have a passing familiarity with the literature and subject matter. The goal for the summer is for the intern to contribute results to a publication in a peer-reviewed journal.

Ken Johnson

Chemical Sensors: The Chemical Sensors Lab develops chemical sensors for nutrients, pH, carbon and oxygen, and deploys these instruments throughout the world in environments from coastal lagoons influenced by agricultural runoff to the high latitudes of the Arctic Ocean and Southern Ocean. There are opportunities to contribute to sensor development and validation and analysis of multi-year data records.

Bill Kirkwood

Shearwater—a novel over-the-horizon mission platform: The Shearwater project is intended to address a number of factors that are currently impacting the science community internal and external to MBARI. The list of issues includes: ever-increasing costs, limits to maximizing operational efficiency of an asset, reduction of carbon footprint by using energy in a more efficient manner, the limitations of using a human crew, and to work around, as least in part, the need for future access to the ocean and an aging fleet both at MBARI and within the US academic fleet.

This summer intern project will continue the efforts to date in studying this new type of platform. The candidate should have an engineering background in mechanical or mechatronics engineering with skills in computer aided design (Solidworks preferred), an understanding of systems engineering, and a minimum of classroom experience in performing analytical trade studies. The candidate must be able to work with engineering students external to MBARI and potentially travel short distances. The current project plan includes building a full-scale mock-up of the selected components and sub-systems, establishing a weight and balance document, energy use analysis, materials selection, as well as various other elements as needed to complete the in-progress feasibility report. Additionally the candidate will assist in producing an as built cost estimate. This work will be used as the core material in writing future proposals to obtain funding for the design and construction of a fully operational system. The ability to work with Navy personnel on a US Navy Base is a must and the successful candidate will be required to sign a non-disclosure agreement. A willingness to work in the model shop and perform hands-on tasks is highly desirable.

Gene Massion

Profiling float for coastal oceanography applications: MBARI is developing a profiling float for coastal oceanography applications. This float is being designed to acquire scientific data autonomously in the coastal regions of the world's oceans for durations in excess of 3 years. We hope to be deploying the first prototypes of this instrument in the summer of 2013. Intern activities may include participation in the control algorithm and mission execution software development for the at-sea prototype, design development and refinement of mechanical and electrical elements of the profiler, and data analysis for all of the above. The ideal candidate would have some background in control systems as well as one of the following areas; Mechanical Engineering, Electrical Engineering or Robotics. Experience with any of the following tools will also be valuable; embedded software development in C/C++, Matlab, Labview, Solidworks, and Solidworks Simulation.

George Matsumoto

Intern Logistical Coordinator: This intern will be assisting with the MBARI intern program. This will likely include assisting the interns with travel logistics during the program as well as coordinating some educational activities on the weekends. It is expected that this intern will also be working on his or her own independent research project. The successful applicant will be an alumna/alumnus of the MBARI intern program and will stay in the same housing as the interns. Letters of recommendation are not required, but please elaborate in your application letter on your proposed research project for the summer.

Mike McCann

Geospatial database administration: With growing capabilities to measure the ocean environment we also have a growing need to intelligently manage the way data are archived for access. This project is concerned with administering high-performance open source relational databases for efficient access to diverse collections of oceanographic data. Supporting systems that are sustainable and that interoperate well with other data systems is a primary concern. Well managed data archives enable scientific understanding and help support good decision making. The intern working on this project will become familiar with PostGIS databases on large server clusters and work with software engineers and information system professionals on administering and tuning these systems.

Tom O'Reilly, Kent Headley, and Duane Edgington

Embedded software engineering: MBARI has developed a new standard for oceanographic instruments. OGC PUCK protocol addresses installation and configuration challenges for sensors by defining a standard instrument protocol to store and automatically retrieve metadata and other information from the instrument device itself.

Most sensor networks require careful manual installation and configuration by technicians to assure that software components are properly associated with the physical instruments that they represent. Instrument driver software, configuration files, and metadata describing the instrument and its capabilities must be manually installed and associated with a physical instrument port. Sometimes these manual procedures must be performed under physically challenging conditions, increasing the chances of human error. PUCK addresses these challenges by defining a standard instrument protocol to retrieve metadata and other information from the device itself. This information can include OGC SWE SensorML and IEEE 1451 Transducer Electronic Data Sheet (TEDS) documents, as well as actual instrument driver code. Computers on the network can use the PUCK protocol to retrieve this information from installed instruments and utilize it appropriately, e.g. to automatically identify, configure, and operate the instruments. Thus PUCK enables automatic self-configuring "plug-and-work" sensor networks.

The standard protocol has been defined for instruments with RS-232 and Ethernet interfaces. Thus far several manufacturers have implemented OGC PUCK for RS-232 instruments. MBARI has implemented a prototype for Ethernet instruments in collaboration with partners at the Polytechnical Institute of Catalunya.  The prototype is based on the Stellaris ARM-Cortex micro controller, and is nearly compliant with the standard, but several additional PUCK features must be implemented. We seek a talented intern with embedded software and electrical engineering skills to refine the prototype and develop tools to rigorously verify compliance with the OGC PUCK standard.

Bruce Robison

Midwater ecology: An intern will have the opportunity to develop a project compatible with the lab's several ongoing research projects concerning mesopelagic and bathypelagic animals. Our lab team is currently working on the ecology, physiology, behavior and systematics of a number of midwater groups, including squids, crustaceans, fishes, and gelatinous zooplankton. Intern projects may involve ROV use, our extensive archive of quantitative video and hydrographic data, and the seawater lab. Typically, we have several possible projects that we think are feasible for the summer's work and we discuss them with the intern, who can select one of them or suggest another.

Ken Smith, Alana Sherman, and Linda Kuhnz

Monitoring changes in the deep-seafloor community using time-lapse photography: This project will examine changes in the dominant megafauna and sediment structures over a period of more than 23 years by analyzing hourly photographs of the seafloor. Past changes at this deep-sea site at approximately 4,000 meters depth have been linked to variation in climate and the food supply which originates in surface waters and ultimately reaches the deep ocean. Other possible links to be examined include the impact of the March 2011 Japanese earthquake and resulting tsunami on this deep-sea community.

Alexandra Worden

Phytoplankton diversity:Phytoplankton are critical to the global carbon cycle – and the health of our planet. This internship is focused on bioinformatic and statistical analyses of large datasets that address phytoplankton diversity. The goal is to understanding phytoplankton communities and changes in their composition. Familiarity with perl and R will be useful but not required, basic molecular techniques will also be helpful.

Last updated: Jan. 31, 2013