2019 Projects and Mentors
Applications for 2019 will be accepted until February 11th, 2019 (1200 hours PST)
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, 2019, 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. Another area of climate change studies we will be involved with are field experiments on the effects of ocean acidification on nearshore animals using our “Free Ocean CO2 Enrichment” (FOCE) system. This system, still under development, allow us to simulate future ocean acidification in small chambers on the seafloor off Hopkins Marine Station, in 15 m deep water, thereby exposing animals to future conditions in their natural habitat. Candidates for the FOCE studies will require a scientific diving certificate, though this is not required for laboratory studies of coastal upwelling. Please include confirmation of Scientific Diving qualification if you are applying for this project.
Jim Birch and Kevan Yamahara
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).
Coastal upwelling in relation to climate variability and change: The California Current System experiences a high degree of variability in part due to episodic coastal upwelling events but also due to phenomena like El Niño and the Pacific Decadal Oscillation. 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. New technologies based on genomics are currently being developed but there are uncertainties regarding how they relate to traditional means and what exactly they capture. This project will choose an area of uncertainty and seek to improve our understanding of the strength and limitations of these new techniques.
Danelle Cline and John Ryan
Passive acoustic monitoring research: During summer 2015 MBARI began collecting passive acoustic monitoring (PAM) data using a hydrophone on the MARS cabled observatory. These recordings have proven the MARS location to be effective for listening to vocalizations of many species. PAM generates very large data sets, and automated methods of signal detection are important to successful research. This intern project will focus on testing methods for automated detection and classification of marine mammal vocalizations, including baleen and toothed whales. This may include exploring feature selection or adapting more generic approaches, like deep learning, to identify species by sound. A background in computer science is required. Experience with acoustic data and/or development with Python scikit-learn 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. Consequences of this process include an increase in the dissolved inorganic carbon content and a decline 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 Saildrone) and platforms (e.g., moored buoys).
We are looking for an intern to join our team and assist in instrument development through laboratory testing, field trials, and data analysis. The intern will 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.
Nancy Jacobsen Stout and the MBARI Video Lab
Data from the deep-sea: MBARI uses high-resolution video equipment to record hundreds of underwater research missions each year. Since 1988, more than 25,000 hours of videotape have been archived, annotated, and maintained as a centralized institutional resource. This video library contains detailed footage of the biological, chemical, geological, and physical aspects of the Monterey Bay submarine canyon and other areas including the Pacific Northwest, Northern California, Hawaii, and the Gulf of California. MBARI has developed the Video Annotation and Reference System (VARS), the Deep-Sea Guide (DSG), and other asset management tools that facilitate the creation, storage, and retrieval of video annotation records from our ROVs, AUVs, and other underwater platforms. We are seeking an intern with experience in conducting ecological studies and/or data sciences to design and complete a project (e.g., research project, website, data products/tools, new analysis/study designs) with a focus on identifying and analyzing data trends, evaluating data quality, and devising methods for strengthening quality, usability, and access of these valuable deep-sea ecological data. Experience working with imagery data, including machine learning, would be beneficial. Applications from CSUMB UROC students are encouraged.
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.
Archived data analytics: Oceanographers have long dealt with large quantities of data from satellites and numerical models – we are now also dealing with large amounts of diverse data from observational platforms. This project is concerned with improving the way we manage, analyze, and visualize oceanographic data form past observational campaigns. Well-managed data archives enable scientific understanding and help support good decision making by both people and robots. The intern working on this project will employ machine learning techniques to improve our ability to extract scientific insight from MBARI’s data archives. Expertise and/or strong desire to program in Python and familiarity with modern web technology will help the intern be successful with this project.
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 following:
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 power consumption.
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, 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.
1) Bio-Electric Field Instrument: MBARI is working on an ultra sensitive electric field instrument with the goal of detecting the electric fields generated by life in the ocean. We are in the feasibility stage and looking for an intern with strong interest in this area. The intern will assist with experiment setup and making measurements in a electro-magnetic shielded aquarium. An understanding of electro-reception in elasmobranchs (sharks, et al) would be good and /or some knowledge or a desire to learn electronic amplifier design and measurement techniques.
2) Real time, high performance processing, at sea on solar powered Waveglider: Real time identification of plankton images generated by a microscope in a waveglider towbody. We are building a microscope with a machine vision camera that is connected to an NVidia Tegra TX2 housed in a towbody. We are using convolutional neural network models (deep learning) trained on a workstation with four NVidia Titan X and a large collection of plankton images. There are many opportunities to add value to this project depending on experience. Skill set would be proficiency with Python, some experience with deep learning and image recognition is desired. There is also opportunity to work with the integrated package and deploy and recovery of the Waveglider towbody and analsis of the recorded images.
3) SharkCafe Cam: MBARI has developed the SharkCafe Cam. We are working to publish the open source package which documents procedures, mechanical and electrical designs and software. Our target audience for the open source publishing is graduate researchers who are wanting to build or modify the SharkCafe Cam. The intern would not only be improving the web page with the documentation and source code but going through the build procedures and creating a SharkCafe Cam.
Midwater ecology: An intern will have the opportunity to develop a project compatible with 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.
Carlos Rueda and Brett Hobson
TethysL: Long-range AUV mission scripting made easy: The Long-Range Autonomous Underwater Vehicle (LRAUV) Group is looking for an intern to work on a Human-Computer Interaction project called TethysL. Since 2008 MBARI has invested significantly in the development of the LRAUV, which fills a niche for week-long higher payload biogeochemical surveys and field programs. A core component of the system is the ability to define, maintain and execute mission scripts against the LRAUV. Leveraging the underlying XML-based mechanisms for mission definition and maintenance within the LRAUV ecosystem, we have recently started the development of TethysL, a domain specific language and a “smart” web-based editor to improve the authoring of LRAUV mission files in a user-friendly and less error-prone fashion. Depending on the intern interest and alignment of potential approach with the overall LRAUV ecosystem, we seek to improve the TethysL component (currently implemented in Scala/ScalaJS, with github.com/lihaoyi/fastparse as core parsing library), and are open to look into alternative approaches (e.g., JetBrains’ MPS) as deemed appropriate. More details about TethysL can be found at https://docs.mbari.org/tethysl. Software Engineering skills required and computer science background strongly preferred.
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.
Microbes active in Deep Sea Sediments: Our lab is interested in the microbial players and mechanisms of organic matter degradation in deep sea sediments. Standard approaches to catalog diversity based on molecular methods fail to distinguish between detrital, free DNA (i.e. remnants of microbes that lived far up in the water column) and ‘live’ DNA (i.e. from organisms alive in the sediment at the time of sampling). In this project we will evaluate if ‘viability PCR’, a technique employed to catalog living microbes in soil and other environments, can be used for marine samples and in particular deep sea sediments. The ideal candidate will have prior experience with standard molecular biology lab techniques (e.g. DNA extraction, PCR) and an interest in microbial ecology.
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.
Multi-vehicle targeted sampling: We develop targeted sampling methods to enable autonomous underwater and surface vehicles to autonomously detect oceanic features and adapt platform behavior to optimally characterize, track, and sample the features. Targeted sampling capabilities allow researchers to direct a limited number of marine assets to specific regions of interest and collect desired measurements/samples absent a human presence. These methods have been applied in a series of field programs and made unique contributions to studies of coastal upwelling systems and microbiology in subtropical eddies. Moving forward, we seek to maximize targeted sampling gain by multi-vehicle collaboration. This intern project provides an opportunity of assisting the LRAUV team in designing multi-vehicle targeted sampling missions and field tests. Training background in electrical engineering and computer science is required. Oceanography knowledge and experience is a plus.