2021 Projects and Mentors
Applications for summer 2021 (June 7 – August 13) are no longer being accepted.
Applications had to be received by 5 pm PST (1700 hours) on February 22nd, 2021. Electronic submissions to email@example.com are preferred. Incomplete or late applications may not be considered. We have added some additional application information that may help you in completing your application.
Clearly identifying a specific research interest/area is an essential part of the application process. Additional projects may be added so please check this page prior to submitting your internship application. 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.
Your application must include
* A cover letter with:
- your general or overall research interests and/or goals,
- your specific research interests and/or goals relevant to MBARI,
- which project you are applying for,
- complete contact information, and
- any relevant coursework and grades received.
* Three letters of recommendation
* A curriculum vitae
* And a completed online supplemental information form
Note: PDF format is preferred for all documents and please put your name in the subject heading for all emails and ask those that are writing letters for you to do the same. Letters can be addressed to the Selection Committee.
MBARI is an equal opportunity employer.
Jim Barry and Steve Litvin
Biology and Ecology of Seamount Ecosystems: Research on the biology and ecology of seamount ecosystems, including coral and sponge communities at Sur Ridge off Central California and octopus breeding colonies at hydrothermal warm springs along the foothills of Davidson Seamount are a central focus of research in our lab. Our research ranges from linkages between ocean conditions (e.g., currents, oxygen, temperature, pH, carbon flux) and coral distribution and conditions, to the biology of breeding octopuses. We use various platforms (ROVs, AUVs, oceanographic moorings) and sensors (imaging systems, current meters, chemical sensors) to observe and measure these ecosystems. Opportunities in our lab for a summer internship would fall within this spectrum of research, including analysis of video imagery in relation to high resolution mapping data, the association of corals with current patterns across Sur Ridge, or the biology of animals inhabiting warm springs at the base of Davidson Seamount.
Jim Birch and Kevan Yamahara
Environmental DNA: We invite an intern that has interests in the collection, processing, and interpretation of environmental DNA (eDNA), the genetic material shed into the aquatic environment by all animals. We are a group of engineers and molecular biologists who develop technology to automate sample collection and processing. In this particular project, we want to see if eDNA can be used to quantify both native and invasive species of fish in Central California coastal streams. Ideally, an intern candidate would have basic molecular biology bench skills (e.g., pipetting, running qPCR) and have an interest in field work and feel comfortable working with developing technology (i.e., robots). This project is not suitable for a virtual program.
David Caress and Eric Martin
Seafloor Mapping and Imaging: MBARI is developing a capability for efficient centimeter-scale surveys of the deep ocean seafloor. Our prototype survey system combines multibeam sonar, scanning lidar, color stereo photography, and inertial navigation. These sensors are operated from remotely operated vehicles (ROVs) at stand-off distances of about three meters. A variety of project topics are possible utilizing surveys from: (1) chemosynthetic communities found around hydrothermal vent fields, and (2) deep-sea coral and sponge communities. Efforts include improving 3D survey path planning, sensor calibration and co-registration of the acoustic and optical data, as well as data processing. The work will combine elements of optimization, image processing, machine vision, and software development. Candidates should have basic competence in C/C++ and Python programming.
The California Current System (CCS) in relation to climate variability and change: The CCS experiences a high degree of variability in part due to episodic coastal upwelling events but also due to climate variability due to El Niño and the Pacific Decadal Oscillation. And anthropogenic impacts are becoming visible. MBARI’s coastal observations have provided, and continue to provide, invaluable time-series measurements of physical, biological, and chemical oceanographic processes relevant to understanding how ocean ecosystems respond to change. This project will involve a combination of data analyses, research and scientific writing, to characterize observations and to further the growing body of literature. Opportunities to work in the field will also be available.
Observational genomics: Our understanding of life in the sea in terms of who is there and how it is changing is limited by our power to observe it. This summer internship will focus on the use of environmental DNA (eDNA) metabarcoding to improve our understanding of marine ecosystems. The project will focus on analyzing datasets and/or on improving/developing laboratory techniques and analytical software capabilities. The successful applicant will have experience with molecular methods, laboratory procedures and programming (e.g. R and Python). Opportunities for field collections may be offered.
Automated classification of deep-sea imagery: MBARI has a rich collection of underwater video and photographs, much of which has been professionally analyzed and curated. We are exploring state-of-the-art automated classification and analysis techniques. This intern will join us in this exploration, testing selected techniques against collections of underwater videos or images to detect and classify organisms of interest to MBARI scientists. One area we are exploring is weakly supervised methods. A background in computer science is required; coursework or experience in machine learning and computer vision would be an ideal background.
Bioluminescence and jellies: This intern will select from a range of topics related to the biodiversity, ecology, bioluminescence, and fluorescence of gelatinous zooplankton. Depending on the intern’s specific interests, the project could involve molecular biology and sequence analysis, behavior, morphology, chemistry, processing of oceanographic data, or analysis of transcriptome data from a variety of deep-sea organisms. For an interested candidate, there is also a possibility of contributing to the development of a plankton web page. 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.
Wave-Energy Converter Modeling and Analysis: We seek an intern with interests in wave-energy conversion and advanced analytic skills to assist with the refinement of numerical models of the MBARI wave-energy converter. The MBARI wave-energy device is a device dedicated to powering oceanographic instrumentation, as opposed to grid-scale wave energy. We are refining the fidelity of the numerical models of this system to support several initiatives and collaborations. The successful applicant will perform boundary element method calculations in WAMIT or a similar tool, analyze test results from both lab tests and field tests, and contribute results to team meetings. This position requires a self-starter who can fit into the existing team and work well independently.
Bioinspired Design:As organisms live and develop in a changing fluid environment, how do these environmental interactions impact their ecology and behavior, and how can we learn from these strategies for application to bio-inspired design? Potential intern projects will use an integrated design, ecological, and engineering approach to either in-situ or ex-situ methods; we will bring the laboratory into the ocean by developing advanced illumination, imaging and sensing tools for ROVs or AUVs that provide insight on how marine organisms function within their natural environment. Conversely, we will bring the ocean into the laboratory through capture of imaging data on live specimens in the lab, using advanced analysis tools to reveal their structure and biomechanics, and developing mechanical mimics of flexible structures found in the ocean.
Position Controller for AUV: This is a project to develop a Line of Sight Position Controller (LoSPC) for MBARI’s Long Range AUV (LRAUV), https://www.mbari.org/at-sea/vehicles/autonomous-underwater-vehicles/long-range-auv-tethys/.
When the AUV is launched, or about to be recovered, it would sometimes be helpful to have a joystick controller to drive the AUV’s thruster and control surfaces to help position the vehicle relative to a ship, or shore-based launch/recovery site. The design of the LoSPC will require experience in hardware selection and integration, software API integration, software safety interlocks, and functional testing. It’s worth noting that some AUVs and Autonomous Surface Vessels (ASVs) already have this remote control driving option, so some research into the existing designs and the availability of Commercial Off The Shelf (COTS) parts will be necessary.
Astrid Leitner and Bruce Robison
Midwater ecology: 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. A potential project focuses on krill which are an abundant and important vertically migrating member of the midwater community in the Monterey Bay, and they sustain important predators like whales and rockfishes that take advantage krill swarms which can form in the canyon. We are interested in studying where in the bay krill swarms have been observed in the past by analyzing MBARI’s extensive video database, identifying any potential krill hotspots, and if ship logistics and scheduling allows, exploring one or more of these hotspots with one of MBARI’s remotely operated vehicles. This project is not suitable for a virtual program.
Autonomous coastal profiling float (CPF): We have a broad spectrum of potential projects spanning a range of disciplines suitable for a summer intern. We are looking for an intern with some experience and a strong interest in any of the following and a particular interest in developing technology for oceanographic research applications.
1) Design and development of embedded microcontroller based systems. The ST Micro STM32 family is of particular interest.
2) Design and development of embedded C# or C/C++ software. Training and/or experience in rigorous software testing methodologies is of particular interest.
3) Labview based automated test systems and web based applications.
4) Design and analysis of pressure vessels. We are particularly interested
in exploring the use of carbon fiber for a new pressure vessel.
Intern logistical coordinator: This intern will be assisting with the MBARI intern program. This will likely include travel logistics during the program as well as coordinating some weekend educational activities. It is expected that this intern will also be working on his or her own independent research project. The successful applicant will have been a past intern in 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.
GO-BGC Adopt-A-Float project: This intern would be responsible for helping to coordinate the Adopt-A-Float program and assist with outreach to educators and other interested partners. This intern would be sponsored by the National Science Foundation as part of the Global Ocean Biogeochemistry Array program and in association with the NSF funded Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) project.
Computational Microscopy Project: Help construct a prototype low cost lensless microscope and explore computational imaging techniques for underwater in-situ plankton recording. We will utilize inexpensive hardware such as NVidia Nano, Raspberry Pi Zero, or OpenMV board, potted for use underwater for image acquisition. NVidia GPU hardware will be available for developing and running the computational imaging algorithms. Stretch goal will be to run algorithms on the embedded hardware in real-time. Access to a benchtop seawater flume for testing with glass beads and plankton. Ideal candidate has knowledge and skills with computational imaging and is looking for an exciting application of those skills for visualizing the microscopic domain of the ocean.
Workflow optimization for eDNA Bioinformatics Project: Improve the automation (scripting, etc) and performance of GPU enabled Basic Local Alignment Search Tool (BLAST) for our workflow that goes from eDNA sequence data from the Oxford Nanopore MinION to organism identification. Skills in computer science or computational biology that include Linux, Bash, Python, C/C++, NVidia GPU programming are a plus. A basic understanding of DNA analysis techniques and DNA barcoding along with the ability to work with and assist biologists in processing data sets will be beneficial.
Zooplankton hotspots in the California Current: This project will participate in a NASA-funded study that aims to predict zooplankton and ecosystem hotspots from satellite data. A 1993-present monthly retrospective of zooplankton maps along the US west coast is now available, and can be used to describe hotspot spatio-temporal variability. The intern will choose a topic related to zooplankton hotspots, using either the satellite-based restrospective, outputs from a coupled physical/biological model, and/or in situ surveys. Possible research topics include, but are not limited to, links between hotspots and top predators such as whales and seabirds, validation of the satellite-based product using in situ surveys, description of hotspots spatio-temporal variability and drivers, contrasted analysis of zooplankton vs phytoplankton. Preference will be given to applicants with experience in Matlab, R or python programming. The internship is computer-based and could be virtual if needed.
Tom O’Reilly, John Ryan, and Steve Haddock
Uncrewed Aerial Vehicles: MBARI is developing a program to use uncrewed aerial vehicles (UAVs) for science and marine operations. Many applications rely on either UAV still imagery or video of animals, plankton blooms, thermal fronts, and other targets on the ocean surface. Imagers may acquire data in RGB, or multiple bands spanning the visible and infrared spectrum. Several thousand still images may be acquired on a typical mission, and it is tedious and cost-prohibitive to manually look for objects of interest in each image. Moreover some images will be blurred, under- or over-exposed, obscured by fog or sunglint, or otherwise not useful to application objectives. Only a subset of mission images will contain targets of interest, such as jellies, fish, or plankton blooms; these targets must be distinguished from floating debris, boats, and image artifacts. Image and target appearance will vary depending on the camera’s spectral bands. This project will investigate image recognition and machine learning techniques to recognize which images are most useful to application goals based on image quality and which images contain targets of interest. The intern will investigate UAV over-water datasets collected with a variety of imagers, such as RGB and thermal infrared cameras.
Madison Pobis and Susan von Thun
Science Communication Intern: This project is ideal for an intern with experience in translating science and technology concepts into written and visual content for the general public. The intern will work with MBARI staff, scientists, and engineers to develop stories about MBARI research. Responsibilities will include creating content from MBARI’s image and video archive and developing compelling stories about our research for our website and social media outlets. We are seeking a candidate with a background in outreach and communication, preferably with interests in science and technology. Strong writing and editing skills are required. Skills in web editing, video editing, other visual content creation (i.e. animations, infographics, illustrations) and photography are desired, but not required. Applications may include writing samples and a portfolio in addition to the other required materials.
John Ryan and Danelle Cline
Ocean Soundscape Research: The ocean holds a world of sound generated by marine life, the earth, and human activities. MBARI has been recording sound in the center of Monterey Bay National Marine Sanctuary for over four years using a hydrophone (underwater microphone), a little instrument that produces big data – about 24 Terabytes per year. Understanding the information contained within this mountain of data requires automated signal processing and machine learning methods that can be used to detect and classify specific sound sources and characterize their variation through time. This project will offer the intern multiple opportunities in ongoing development and application of sound analysis, including studies of cetaceans, earthquakes, shipping noise, and sound occurrence patterns that emerge from statistical analyses of the sound archive. This work may include exploring unsupervised learning for data exploration and labeling or supervised learning using convolutional neural network architectures. A background in computer science is essential. Experience with acoustic data and/or development with Tensorflow or Pytorch will be advantageous.
MBARI Media Management: MBARI has over 27,000 hours of underwater video recorded by remotely operated vehicles (ROVs) and autonomous underwater vehicles (AUVs). This video archive has been expertly curated and annotated and these annotations have provided data for over 400 peer-reviewed science publications. Recent developments in Machine Learning (ML) create opportunities to automate video analysis, however, tooling and workflows are needed to validate and integrate ML with our annotation data systems. The intern will work closely with researchers and software engineers to explore novel methods to validate, analyze, visualize, and present the video and annotations to scientists, researchers, and the public. Applications for this internship should have coursework/background in computer programming. Skills in statistics, data visualization, databases, and/or web development are desired, but not required.
Ken Smith and Crissy Huffard
Climate change and deep-sea community structure: Using a 29 year time series study at 4,000 meters depth in the eastern North Pacific, we have found significant changes in the surface ocean processes related to food supply and benthic community responses at these abyssal depths. Time-series photographs taken hourly of the sea floor have shown major shifts in population densities and biomass amongst many dominant species of megafauna. Many megafauna have shown precipitous changes in population abundance and size over the entire time series that began in 1989. This intern project will examine the latest changes in megafauna populations over the time series, in relation to on-going changes in climate and upper ocean processes determined from satellite monitoring.
Coastal Biogeochemical Sensing Program: This program focuses on development and application of novel autonomous biogeochemical sensors to effectively monitor the coastal ocean. Biogeochemical cycles in coastal oceans worldwide are experiencing unprecedented alterations due to anthropogenic activity, such as eutrophication, deoxygenation, and ocean acidification. Understanding the drivers for these changes are critical to establish baselines and make accurate projections on how they will change in the future, and thus ultimately learning how to manage coastal oceans effectively. Autonomous sensors equipped on appropriate platforms provide an effective tool to monitor this highly variable system. During the summer, the intern can be involved in a variety of different aspects of sensor developments, including but not limited to electrical/software design of benchtop prototypes, deployment and recovery in nearby field sites, to interpreting new data form autonomous platforms such as gliders and floats.