Monterey Bay Aquarium Research Institute

Application procedure:

The application period for the MBARI 2010 Summer Internship Program is now closed. Applications should include a cover letter, a curriculum vitae, three letters of recommendation, and we would also like you to complete an online form. The cover letter should include a statement of your research interests (with specific mention of one of the following potential projects or areas), relevant coursework and grades, and complete contact details (home and work phone numbers and email address).. MBARI is an equal opportunity employer.

Below you will find 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. I have provided links to the mentors' home pages (if available) so that you can learn more about the various mentors, please DO NOT contact the mentor directly.

Application materials (including letters) can be sent to MBARI via fax (831-775-1620), regular post, or by email. If you opt for an email application, please send your materials directly to George ( and copy Cynthia Ogg (


Nancy Barr

Science and Technology Illustration: MBARI is seeking an intern with experience in translating science and technology concepts into visual media. The intern would likely work on several different projects during the summer, and possibly in different formats (drawing, animation, digital art, etc.). Applications should include a portfolio (hard copy or digital) in addition to the other required material.

Web Design and Development: This project would involve creating web pages and/or interactive features for viewing images or data produced by our science and engineering projects. Final products would be designed in keeping with MBARI website style guidelines and best practices for usability and accessibility.

Jim Barry

Life in a high-CO2 ocean: This project would focus on studying the effects of a high-CO2 ocean (ocean acidification, hypoxia, warming) on marine animals. The intern would collect information on ongoing (and past) ocean acidification research and integrate it with a Google map. With this we could view what sort of activities are going on in the world in this topic.  This internship could also include field and laboratory studies of the physiological response of animals during experiments simulating future ocean conditions.

Jim Bellingham

Autonomous Underwater Vehicle: There are a number of potential options including, but not limited to: (1) Exploration of a deep-water design variant of Tethys; (2) Developing a graphical user interface for XML-schema based mission development on Tethys (our long range AUV);  (3) Developing test missions for Tethys (for execution primarily in the simulation environment, but also on the vehicle) that verify the operation of all possible mission behaviors; (4) Design/develop the Tethys system test set. Test missions will be executed on a benchtop target and system validation will be performed using (mostly) automated test drivers written in Python. This task would require an interest in hardware/software integration, familiarity with the Linux OS, and basic programming skills; (5) Embedded PIC programming. Develop and test the load controller software. The existing code base will be altered to meet current requirements and updated schematic. A test plan will be developed and the load control subsystem validated.…and for something completely different…(6) Behavioral modeling of organisms using AUV reflexive control architecture,

Advanced sampling methodologies with underwater robots (AUVs)
: Robotic platforms (such as AUVs) are revolutionizing our ability to sample ocean processes. Most historic AUV operations were along pre-defined mission transects. We are interested in developing a new generation of mission plans that will exploit the synergy between on-board sensing capabilities of the vehicle and vehicle’s mobility. We are looking for a person with strong programming and data analysis (or signal processing/machine learning) skills to analyze historic AUV datasets and develop prototypes of new sampling strategies for MBARI’s DORADO and Thetus AUV’s. During the course of the internship, intern will be exposed to the cutting-edge ocean sampling technologies and will develop strong data analysis skills.

Larry Bird

Effective Shackle for ROV Manipulator Operations: Cabled Seafloor Observatories have the potential to revolutionize oceanography.  Key components of these observatories are the connectors and cables that allow interconnection with scientific instruments.  Quite often these cables and connectors are required to be shackled to a central node or outlying experiment to protect and assure the integrity of the system. A need exists for the development of a shackle that can easily be set/unset using Remotely operated vehicle (ROV) manipulators, employing materials that address a marine environment. The successful design and development of this load-rated shackle system will require establishing the requirements with MBARI marine operations. CAD modeling, interaction with engineering/manufacturing personnel, and testing will also be required.

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. We will put this together for a cruise on The RV Western Flyer in July to explore the waters off southern California. A summer intern will be engaged in a specific aspect of this based upon abilities and experience.

Francisco Chavez

Analysis and Modeling of Decadal Changes: Potential intern projects include the analysis of a variety of environmental information collected at MBARI as well as model simulations to determine the mechanisms responsible for observed interannual to decadal changes and/or trends. One particular trend is a steady decrease in dissolved oxygen at depth that has occurred over the last decade. Is this decrease due to large scale changes in ocean circulation or to local increase in primary productivity or both?

David Clague

Submarine Volcanism: Projects in the broad area of submarine volcanism are possible. Our work over the last few years has focused on submarine explosive volcanic activity, mainly using samples of volcanic fragments deposited both near and away from submarine eruptive vents. We continue work on these samples to obtain geochemical and age data. We have also been collecting new high-resolution (1-meter) multibeam mapping data from the MBARI Mapping Autonomous Underwater Vehicle (AUV) for several years and have a number of data sets along portions of the Juan de Fuca and Gorda mid-ocean ridges, and from Davidson Seamount. Our goal is to develop geologic maps at each of these sites using the bathymetry, observations, and samples from our remotely operated vehicles (ROV), and age data on flows. Additional AUV mapping is planned for early 2010 to map several near-ridge seamounts with large calderas in the Taney chain offshore Monterey, and several other seamounts near the CA margin. Processing and interpreting some of these data could be summer projects. Near the end of the internship, we have a planned nine-day cruise to sample some of these seamounts that would provide the opportunity to go to sea on the Western Flyer using the ROV Doc Ricketts.  

Danelle Cline and Duane Edgington

Automated Visual Event Detection: Our project involves implementing  a computer vision system that analyzes images collected by observatory cameras or underwater vehicles to detect, classify, and identify organisms.  We are collaborating with labs at California Institute of Technology and University of Southern California to adapt and extend computer vision systems modeled after the human visual system. The internship  involves working with a small team, participating in development, and analysis of still frames captured from a deep-water site in Monterey Bay. We welcome applicants with a background in computer science,  machine vision, or marine biology. See our AVED project web site.

Danelle Cline, Duane Edgington, and George Matsumoto

Information Dissemination from Eye-in-the-Sea on MARS: Our project involves work on information dissemination from a deep-ocean video camera, Eye-in-the-Sea on MARS.  The project focuses on making the video and data available in a form that will be readily accessible by educators via the Internet.  The internship  involves working with a small team, participating in development,  and analysis of video captured from a deep-water site in Monterey  Bay. We welcome applicants with a background in web publishing, education, computer science, or marine biology.

Kim Fulton-Bennett

Science Writing/Multimedia: The intern will work with MBARI's communications staff to develop web articles and multimedia works describing MBARI research for the general public. The multimedia works could include text, audio, still images, video, and georeferenced links with Google Maps or Google Earth. The intern should have excellent writing skills and a working knowledge of html, as well as a willingness to learn html code necessary to embed multimedia materials on web sites. Knowledge of multimedia authoring tools or Google Earth would be a plus. Please include web links or samples of writing for the general public with your application.

Rich Henthorn

Benthic-Pelagic Biochemical Process Interaction/Process Control and Automation: The project involves adapting autonomous vehicle control software developed for the Benthic Rover to control a new Sedimentation Detection and Imaging System. The objective of the overall project is to develop a Sedimentation Event Sensor to record both visible-light and fluorescence macro-images of collected sediment, thus measuring the quantity and quality of particulate matter (food supply) reaching the seafloor. The system will be deployed on the MARS cabled observatory. The intern will focus on adapting system and control software developed for the MBARI Benthic Rover to manage the experiment process on the new platform. The tasks include creating new device control interfaces, developing process control routines, and data management and automation.
Candidates must (1) have a science and/or engineering background, (2) be proficient in a modern object-oriented programming/scripting language (e.g., Java, C++, Ruby, Python), (3) have good communication skills, and (4) enjoy working as part of a team.

Ken Johnson

Development and Testing of Novel pH Sensors for Long-Tterm Applications in the Ocean: Concern about ocean pH has become a major topic in ocean science. Yet there are no simple, reliable methods for observing pH from autonomous platforms such as moorings, floats or gliders. In 2009 we demonstrated long-term stability of a pH sensor. The major challenge remaining with this sensor is to adapt it for operation at high pressure. We have made considerable progress in understanding the limitations in the sensor packaging, and then testing various new implementations that are designed to address these limitations.

Chad Kecy

FOCE (Free Ocean Carbon Enrichment) Experiment: FOCE requires an upgrade to its existing load-switching functionality. Currently we use a mix of off the shelf PC/104 hardware and in-house designed boards to switch power to the science and engineering instruments on FOCE. We would like to develop a stand-alone load switcher to combine current functionality and add in new features. Functions include load switching, current and voltage monitoring, under-voltage/over-current protection, and interfacing to separate ground faulting boards. This project would be ideal for an electrical engineer proficient in embedded systems as it contains digital hardware design, analog hardware design, and some software (PIC) development. The intern would also oversee and contribute to the board layout and fabrication.

Bill Kirkwood

SWATH Mapping of Shallow Bottoms in Dynamic Conditions: MBARI has worked with students over several years to develop an autonomous small water-plane area twin hull boat. The boat is equipped with an Imagenix™ multi-beam sonar for bathymetric mapping. The project for 2010 is to integrate additional instrumentation and data streams required for enhancement of data quality and map accuracy. After successful instrument integration and testing, the newly configured vehicle will perform a test mission in the Moss Landing harbor. The mapping assignment has been requested by the committee consider the needs of a future MBARI ship. The map will be used to determine the parameters for a new ship that would be based in Moss Landing harbor. This work will also form the basis of the next generation platform looking at sediment transport mechanisms and shifting sandbars in 3 knot currents. The successful candidate should have a background in an engineering discipline, mechatronics, or robotics. Familiarity with MB-System software and bathymetric mapping a plus. Demonstrated analytical skills of dynamic systems using MATLAB required as part of the project. The candidate should also have a demonstrated ability to work in a team environment, as well as strong organizational skills and self-motivation.

Mike McCann

Virtual 3D Worlds: With increasing amounts of diverse oceanographic data being collected and archived, new techniques are required to enable easier interpretation. The intern will develop data visualization tools to enable scientists and engineers to better understand experimental and natural processes encountered with MBARI's operations. We encourage highly motivated applicants with programming and video gaming experience to apply. Preference will be giving to applicants with skills in one of more of the following areas: script programming (Perl, Python, Ruby), 3D modeling tools (X3D, SketchUp), and an oceanography or engineering background.

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.

Thom Maughan and Kanna Rajan

Onboard Autonomy: MBARI's Autonomous Systems Group is engaged in research efforts to use advanced Artificial Intelligence (AI) techniques to enable autonomous underwater vehicles (AUVs) to be more adaptive and contextually aware of their resource and goal commitments. Our onboard deliberative system T-REX being used on an AUV platform, is based on the sense-deliberate-act paradigm synthesizing new mission plans in response to environmental conditions. T-REX uses a state-of-the-art temporal constraint-based planner developed originally at NASA Ames and flown on a number of space missions. Potential projects for summer 2010 include:
(1) An intuitive science interface for mixed-initiative control of AUVs. The resulting code will need to visualize dynamic constraint networks underlying onboard and offboard plans for controlling an AUV asset at sea.
(2) Interface an existing graphical AUV simulation toolkit with T-REX to provide a geographically ground post-facto visualization of T-REX from sea-trials.
(3) Work on oversubscription resource modeling for T-REX. This will require understanding of the internals of T-REX modeling and constraint satisfaction for plan execution.
(4) Work on integrating synthetic ocean model outputs (such as those from ROMS) with trajectory planning for AUVs.
Highly motivated graduate students with substantial Java programming skills, C, or C++ programming skills are encouraged to apply. AI planning and a background in Constraint Satisfaction would be a plus.

Tom O'Reilly

Sensors and Sensor Networks: This project will investigate techniques to integrate instruments into sensor networks, using standards such as IEEE-1451 and Sensor Web Enablement. The project may involve programming at several levels, ranging from Internet "web services" to instrument firmware. The project will especially look at techniques to minimize instrument integration integration effort.

Steve Ramp and Heather Kerkering

The Central and Northern California Ocean Observing System (CeNCOOS): The mission of CeNCOOS (see is to integrate marine observations to inform decision makers and the general public. CeNCOOS produces information products to facilitate science-based management decisions affecting the health of the oceans.  Topics of high interest presently include climate change, marine spatial planning, search and rescue, hazardous material spills, harmful algal blooms, coastal inundation, and water quality.  Summer interns are sought to help implement all aspects of the system including marine observations, data management and communications, operational ocean modeling and prediction, marine policy, education and outreach, and product development.  Potential interns could have a scientific, marine policy, educational, or information technology inclination.  The program is highly flexible and we can suggest specific projects which can be completed during the summer or potential interns may suggest projects of their own. 

Julie Robidart

Environmental Sample Processor (ESP): Microbial dynamics in Monterey Bay are driven by physical and chemical parameters.  The ESP monitors microbial communities in situ and is coupled with instrumentation during deployments that allow investigators to study microbial oceanography in real time.  This summer will be a busy field season.  An intern on the ESP project will qualify molecular assays to quantify microbes that perform important functions in marine biogeochemistry, as well as help with deployments and data acquisition and analyses.  The intern may also aid in development of new assays relevant to Monterey Bay biogeochemistry.

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.

Brian Schlining

MBARI Deep Sea Guide: MBARI has a unique underwater video library cataloging the geologic features, organisms, and elements of MBARI research that occur within the Monterey Bay submarine canyon. We are currently seeking an individual to assist with the development of an on-line "Deep Sea Guide". The goals of the Deep Sea Guide are to create an encyclopedia describing the geology and biology of the Monterey Bay submarine canyon and to leverage video annotations cataloging the video features to present novel and valuable scientific information. The intern will work with a small team to develop a web- based interface to our existing databases. We encourage highly motivated applicants with web development or web design experience to apply. Preference will be given to applicants with skills in one of more of the following areas: graphic design, Java or Groovy programming, web presentation technologies (AJAX, Flex, HTML+CSS, etc.), ocean sciences background.

Ken Smith, Alana Sherman, and Linda Kuhnz

Photo Mosaic Analysis: The Benthic Rover is an autonomous bottom-transecting vehicle that makes long time-series measurements of seafloor processes in addition to taking high-resolution photographs of the benthic community. This instrument has been deployed on the MARS underwater cabled observatory in Monterey Bay over the past six months and has occupied over 40 sites with real-time data acquisition to our lab ashore.  While transiting five meters between each site, the transect camera takes overlapping photographs of the seafloor and conspicuous fauna, providing a long time-series record of spatial and temporal changes at this deep-sea station located at approximately 900 meters depth. These photographic records combined with synoptic measurements of temperature and current velocity, provide an unprecedented data set to be analyzed by a summer student intern

Bob Vrijenhoek and Shannon Williams

Molecular Ecology: The project would focus on harvesting larvae from the deep-sea bone-eating worms, Osedax spp. We will use the larvae to test the Deep Environmental Sampling Processor (DESP), an autonomous underwater molecular lab capable of identifying marine larvae from their nucleic acid signatures. A number of skills will be used including collection of specimens, DNA extraction and sequencing, and statistics.

Alexandra Worden and Sebastian Sudek

Exploring distributions of uncultured algae: Photosynthetic algae are responsible for a significant portion of global CO2 uptake. In marine systems the organisms responsible for this uptake are still not well known. This is very much the case for the eukaryotic picophytoplankton involved in this process, especially in terms of their distributions and contributions. This project will employ molecular techniques to investigate the distribution of an uncultured group of tiny photosynthetic algae, or potentially cultured groups, in environmental samples.

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Last updated: Feb. 10, 2010