Monterey Bay Aquarium Research Institute
2014 MBARI Summer Internship Program

2014 Projects and Mentors:

The application period is now closed.

Jim Bellingham

AUVs that fix themselves: MBARI operates a growing number of Long-Range AUVs. These vehicles may operate for weeks at a time, carrying increasingly sophisticated sensor suites. Our challenge is to make the vehicles capable of handling problems on their own. This internship would involve revisiting past AUV failures and developing ways to detect and mitigate them. The project will involve equal parts data analysis, classifier development, and autonomy. Data analysis will be required for reviewing past problems (we have over 6000hrs of operations, and lots of good problems including shark attacks). Classifier development will be required for finding ways to detect failures with a high probability of detect, and a very low probability of false detect. Finally the autonomy part of the work will revolve around developing methods to mitigate failures. Sensing and sampling microbes with AUVs: MBARI makes extensive use of AUVs to map and sample microbial communities in the marine environment. Sampling payloads include water samplers, and (soon) the 3G ESP. However, our ability to tell when the composition of the microbial community has changed, and therefore should be sampled, is poor. We have a large number of sensors, including devices that measure particle size distribution, acoustic backscatter, and even imaging systems. The challenge is to develop algorithms that can use the sensors data in real time (rather than post processing) to guide sampling.

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 acidification: This project looks at the variation in intertidal and subtidal pH in relation to environmental and biological conditions. It investigates through existing data and new experiments/observations the spatial variability in pH and what roles of physics and biology play in determining the patterns.

Dave Clague and Jenny Paduan

Submarine volcanoes and volcanic islands: We have two potential project ideas: The first project will have the intern utilize 1-m resolution mapping data collected by autonomous vehicle of volcanic terrain on the Juan de Fuca Ridge or northernmost East Pacific Rise. The goal is to reconstruct the volcanic history of a site by evaluating existing ROV dive observations, lava flow age data, and lava geochemistry in the context of the mapping data. The other project would be an intern who is interested in working on carbonate reef rocks from along the Hawaiian Ridge recovered by dredging, submersible, and core drilling. Almost all the lab data exist already, so the project would be developing the relations between dive observations, sample descriptions, age data, and paleoenvironmental parameters from fossil assemblages from drowned coral reefs along the Hawaiian volcanic chain.

Danelle Cline and John Ryan

Automated plankton identification: The project involves investigating various pattern recognition and machine learning methods to help aid in the automated identification of plankton from images. Student will be working with images collected from the world's first commercially available submersible digital holographic particle imaging system. The internship involves comparing various methods with expert classification, and participating in the development of new methods. An understanding of machine learning methods and a basic understanding of plankton a plus, although not required.

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.

Julio Harvey

Molecular detection and ecology of marine zooplankton and phytoplankton: The qualifying intern will be directly involved in molecular genetic aspects of sampling and identifying marine zooplankton (SIMZ), an ongoing project in the Vrijenhoek laboratory. In particular, testing molecular probes designed to detect zooplankton (invertebrate larvae and copepods), against both pure cultures and environmental samples in addition to screening samples collected by the AUV Dorado or through more traditional means, such as plankton nets. Previous experience with molecular methods including genomic isolation, PCR, DNA sequencing and bacterial cloning is desired. Previous experience with microscopy and invertebrate larval or copepod identification is also welcome. Experimental results will be analyzed along with associated environmental data collected by the AUV, CTD casts or other means to answer fundamental questions regarding how plankton assemblages interact with local oceanographic phenomena in the Monterey Bay. All research conducted will be intended for expeditious publication in a leading peer-reviewed scientific journal.

Richard Henthorn

Benthic rover and sedimentation event sensor refit: MBARI's Station M time-series employs a number of unique instruments designed for deployments lasting months at depths over 4000 meters. Two of these instruments, the Benthic Rover and the Sedimentation Event Sensor, will be returning to MBARI this Spring for refitting that will require some additions and changes to the existing control system and device interface software. This internship will contribute in a number of important ways by designing, implementing and testing device software interfaces, improving existing interfaces and control algorithms, and automating software tests and mission data processing. Candidates should have experience writing and modifying software in a modern, object-oriented computer language (e.g., C/C++, Java, Python, Ruby) and be comfortable working with low-power single board computer hardware and Linux operating systems.

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. The float will be undergoing sea trials in the summer of 2014 and we expect a lot of design refinement and incremental increases in functionality based on our at-sea test program. Intern activities may include participation in the test design, deployments, data analysis and subsequent refinement of the mechanical, electrical and software design of the profiler. 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# (or similar language), Matlab/Simulink, 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

Big ocean data: Big Data Analytics is a growing discipline in the field of information technology. Oceanographers have long dealt with Big Data from satellites and numerical models; we are now also dealing with Big Data from observational platforms. This project is concerned with improving the way we manage and analyze diverse collections of oceanographic data. Well managed data archives enable scientific understanding and help support good decision making. The intern working on this project will become familiar with oceanographic data processing pipelines and work with software engineers and scientists on developing processes for extracting insight from MBARI's data archives.

Charlie Paull and Esther Sumner

Submarine canyon processes: MBARI has been at the forefront of developing state-of-the-art tools to map and sample submarine canyons. These include collecting high resolution maps of the seafloor using autonomous underwater vehicles and using remotely operated vehicles to explore and precisely sample canyon-floor sediments. Over the past decade the floors of numerous canyons along the Californian margin have been mapped and hundreds of sediment cores collected. We offer the intern the opportunity to participate in the integration of these datasets in order to better characterize the nature of the sediment flows that shape these canyon systems. The precise nature of the project will be tailored to the student's interests but could for example involve, sedimentological analysis, bathymetric analysis or numerical modeling.

Tom O'Reilly, Doug Au, and Brian Kieft

Augmented reality applications for shipboard operations: This project will explore augmented reality technologies and head mounted displays (HMDs) to enhance shipboard operational effectiveness. In particular, the intern will develop a prototype Android application for Google Glass or Recon Jet that allows a shipboard user to monitor the location of an autonomous underwater vehicle (AUV). Operators rely on computers to deploy, monitor and recover AUVs, but shipboard environmental conditions pose serious challenges to traditional human-machine interfaces. In heavy sea-state, operators may need to hang onto railings or other fixtures with one or both hands to avoid injury. In this case keyboard and mouse operations are difficult or impossible, and the user may need to set down handheld devices. At times operators may be required to be on deck to observe sea and weather conditions, to spot assets, or other reasons - yet many display screens are unreadable in bright sunlight. We believe that HMDs such as Google Glass and Recon Jet could address these challenges - these devices are designed for outdoor use, and support one-handed or hands-free operation through touchpad, voice recognition, and gaze-detection. Moreover these devices include sensors to measure user orientation, motion, and geographic location in real time, as well as interfaces that connect to the Internet. The prototype application will use these capabilities to provide a user with AUV bearing and range, weather forecast, presence of shipping traffic, and other relevant information. Intern will work with AUV operators to define prototype requirements and evaluate results.
Prerequisites: Applicant must be experienced in writing Android applications, must provide a link to self-developed application(s) Applicant must be willing to go to sea

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.

Leslie Rosenfeld

Cost-benefit analysis of ocean observing: The Central and Northern California Ocean Observing System ( is a collaborative that enables sustained and coordinated measurements, model nowcasts and forecasts, and integrated products to inform decisions about the coastal ocean between Pt. Conception and the OR/CA border. The Center for the Blue Economy at the Monterey Institute for International Studies ( promotes ocean and coastal sustainability by providing the best available information to empower governments, NGOs, businesses, and concerned citizens to make educated decisions about the marine environment. CeNCOOS and CBE are seeking an intern to enhance traditional analyses of data available from CeNCOOS observing/modeling systems with a cost benefit analysis of some subset of the system to support industries or other users within the CeNCOOS region. The elements of the observing/modeling system, and relevant current or potential users of the system and its products, to be included in the new analysis will determined by the intern in concert with CeNCOOS and CBE mentors and partners.

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 continued 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 port the application from the current internal prototype to a beta version on MBARI's external website. 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 and Crissy Huffard.

Monitoring changes in the deep-seafloor community using time-lapse photography: This project will examine changes in the demographics of dominant megafauna over a period of more than 24 years at Station M (~4,000m, at the base of the Monterey Fan). Photographs of the seafloor taken by a moored camera tripod, the Benthic Rover, and a camera sled since 2006 will be analyzed for animal size, abundance, and indicators of reproduction. These data will be compared to historical measures recorded from 1989-2006. A recent study, we just published in the Proceedings of the National Academy of Sciences, has found a significant increase in the food supply to this site in recent years compared to the past two decades. This internship will contribute significantly to the follow-up investigation into how megafauna communities might be responding to these food inputs through growth, reproduction, and immigration. Other possible links to be examined include performing statistical analyses to compare sizing methodologies, and sizing animals using stereo-camera images taken by a remotely operated vehicle.

Robert Vrijenhoek

Genetic connectivity among populations of hydrothermal vent organisms: Relatively short-lived communities of hydrothermal vent organisms are distributed intermittently along the global mid-ocean ridge system. Our goal is to examine the genetic structure of vent-restricted species to common identify geomorphological and hydrodynamic factors that contribute to the connectivity (or isolation) of disjunct animal and bacterial populations. The qualifying intern will be directly involved in laboratory-based molecular population genetic analyses. The project will focus on development and analysis of nuclear DNA markers to complement previous analyses of mitochondrial DNA. Experience with molecular methods including extraction of genomic DNA, PCR, and DNA-sequencing is desired. Some familiarity with basic statistical methods is necessary.

Alexandra Worden

Phytoplankton and energy strategies: The project explores the roles of mixotrophic grazers and other phytoplankton in the microbial food web. Mixotrophs are protists that combine a photosynthetic capacity with the ability to ingest prey organisms and are important predators in diverse marine ecosystems. Topics of investigation could include environmental factors regulating feeding behavior, prey selectivity, or physiological and metabolic changes accompanying a switch in the nutritional strategy of mixotrophs from photosynthesis to grazing or vice versa - as well as overall diversity and physiology of phytoplankton.

Last updated: Feb. 13, 2014