2020 Projects and Mentors
Applications for 2020 are no longer being accepted.
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
MBARI is an equal opportunity employer.
Jim Barry and Steve Litvin
Climate Change: During summer, 2020, our lab plans to focus on projects related to the effects of changing ocean conditions linked to climate change on the performance (measured in various ways – e.g., growth, survival, respiration rates) of nearshore animals. Coastal upwelling brings waters into nearshore areas that are nutrient-rich, stimulating phytoplankton blooms that drive the high productivity of our coastal waters. However, upwelled waters are also more acidic, hypoxic, and colder than surface waters, and can be stressful for a variety of nearshore organisms. Climate warming is driving shifts in ocean conditions leading to upwelling of even more acidic and hypoxic waters and it remains unclear how coastal species will cope with exposure to combinations of changes in pH (ocean acidification), oxygen, and temperature. We use a “Upwelling Simulator” to support laboratory experiments attempting to understand the consequences of current and future upwelling for nearshore species.
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).
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, and is operated from remotely operated vehicles (ROVs) at stand-off distances of about three meters. This project will investigate methods for improving the calibration of these instruments and the co-registration of the acoustic and optical data, with a focus on surveys of deep-sea coral and sponge communities and of the chemosynthetic communities found around hydrothermal vent fields. The work will combine elements of optimization, image processing, machine vision, and software development. Applicants should have basic competence in C and C++ 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 be on the use of environmental DNA (eDNA) metabarcoding to improve our understanding of marine ecosystems. The project may focus on analyzing datasets taken from Monterey Bay, and/or on improving/developing laboratory techniques and analytical software capabilities. The successful applicant will have strengths in molecular methods, laboratory analysis and programming.
Danelle Cline and John Ryan
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.
Duane Edgington and Danelle Cline
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.
Ocean Acidification Instrument Testing and Development: The ocean absorbs ~25% of human-caused carbon dioxide emissions each year, slowing the rate at which greenhouse gasses buildup in the atmosphere. This causes an increase in the dissolved inorganic carbon content and a decreases in the pH of ocean surface waters, commonly referred to as ocean acidification (OA). To monitor OA and study how it may be influencing marine carbon cycling, we are developing an instrument that will measure both the carbon dioxide and dissolved inorganic carbon content of surface waters from autonomous surface vehicles (e.g., Wave Glider) and platforms (e.g., moored buoys).
We are looking for an intern to join our team and assist in instrument development through laboratory testing as well as data analysis. The intern may have opportunities to run instrument trials in the MBARI test tank and conduct field work from small boats and MBARI research vessels. Successful candidates will have some experience with analytical chemistry and be familiar with a programming language (MATLAB or Python) that can be used to analyze data.
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.
Engineering Intern: Be a part of multiple Engineering teams working on demanding development projects. The intern will work with the mentor to design a challenging program of tasks resulting in a thorough understanding of processes and collaboration the student will encounter in “real world” engineering teams. The internship will require the student to work in multiple disciplines (e.g., mechanical design and fabrication, software development, testing, use of graphs and plots) and work in different roles to accomplish project objectives. The program will draw from one or more real MBARI development projects involving
- extreme environments
- climate change
- ocean observing systems
- autonomous vehicles
The ideal candidate will be an engineering student with the ability and desire to learn multiple technical disciplines and excellent communications skills. Minimum third-year undergraduate required.
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 bring the laboratory into the ocean by developing tools and techniques that provide insight on how the marine organism functions within its natural environment or bring the ocean into the laboratory by conducting advanced imaging experiments on live specimens and/or developing mechanical mimics.
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.
Autonomous profiling float: We have a broad range of projects suitable for a summer intern spanning a wide spectrum of disciplines related to our
autonomous profiling float program. Potential projects may include the
1. Development and enhancement of a variety of tools to enhance our testing
program to ensure our profilers will work reliably, unattended for years at
a time. Current tools include an automated benchtop ocean pressure
simulator and a profiling float for long term, shallow water operation in
our 1.5 million liter test tank;
2. Continued improvement of our automated software test framework. This
includes analyzing the existing software, developing a test strategy,
implementing and running test software in the framework and improving the
existing code based on the test results;
3. Improvements to our mission planning and operation system; or
4. Analyzing the current system and developing strategies for minimizing
There will also be opportunities to participate in at-sea testing of the
profiling float. These projects will require an intern with some experience
in one or more of these areas: design and testing of robotic systems,
software design with particular emphasis on software testing. Experience
with any of the following will be a plus. Solidworks, Matlab and Simulink,
Labview, C#, or a similar programming language.
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.
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.
Physical/biological variability in Monterey Bay from AUV data: This project will explore recent, recurring surveys of Monterey Bay by an autonomous underwater vehicle (AUV). Data from AUV Dorado include physical measurements such as temperature and salinity, biological measurements such as fluorescence and bioluminescence, and derived proxies for autotrophic and heterotrophic plankton. The intern will generate products describing the physical/biological variability in Monterey Bay using these data. Topics include, but are not limited to, seasonal variations, interannual variability associated with the “warm blob”, validation of plankton proxies using external datasets, development of new proxies, identification of physical/biological patterns using machine learning. Preference will be given to applicants with experience in Matlab or R programming.
Deep-sea Guide: 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. The intern will work closely with researchers and software engineers to explore novel methods to 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.
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.
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.