2016 Projects and Mentors

Below is 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 essential part of the application process. 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:

  1. your general or overall research interests and/or goals,
  2. your specific research interests and/or goals relevant to MBARI,
  3. which project you are applying for,
  4. complete contact information,
  5. 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.

The application deadline for 2016 has passed. We are no longer accepting applications. Please check back in November 2016 for information about our 2017 Internship Program.

Nancy Barr
Web development/content creation: This intern will create web content to share MBARI projects and developments, whether by gathering and synthesizing existing content or working with the science and engineering staff to create new material. A web development background may be helpful, but editorial and communications experience will prove most valuable. The MBARI website will be transitioned to WordPress before this project begins, so familiarity with WordPress is needed.

Aric Bickel and David Anderson
Web development/communications: This intern will assist in the expansion and development of the communications and education section of the CeNCOOS website (cencoos.org). Depending on experience, the intern may also develop communication products aimed at synthesizing science and monitoring results for specific coastal stakeholders. Experience in web development, science communications, and social media is desired. Experience with content management systems is preferred. The intern will gain experience communicating science to varied audiences (some specific, some broad) and developing interactive communications interfaces. The successful candidate will have the opportunity to work with leading ocean and data scientists to develop methodologies to communicate their science to broader audiences.

Peter Brewer and Ed Peltzer
Laser Raman spectroscopy: Our laboratory team is exploring the use of novel deep-sea laser Raman spectroscopy to reveal the basic chemical physics of life in the deep sea. Gelatinous animals offer an attractive target for their abundance, their transparency allowing penetration of the laser beam, and their relative lack of fluorescence, thus yielding a clean Raman signal. The contrast in the vibrational modes between gelled and liquid water reveals the adaptations and energy cost required for coping with very large ranges of temperature and pressure, and the ability to exclude some salts provides a likely internal osmotic pressure gradient. Measurements in both the laboratory, and in the deep sea, are in progress and the spectra reveal a wealth of information on these ancient life forms.

Francisco Chavez
El Niño: The 2015-16 El Niño is presently underway and has and will continue to result in dramatic ecosystem changes along the California coast and beyond. This project will produce a synthesis of available El Niño information and highlight the most important impacts.

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 (https://www.mbari.org/mars/science/hydrophone.html). 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.

Steve Haddock
Bioluminescence and jellies: Interns will select from a range of topics related to the biodiversity, ecology, bioluminescence, and fluorescence of gelatinous zooplankton. Depending on their 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.

Chad Kecy
SeeStar Open-Source Imaging Project: Over the last three years we have developed a complete open-source underwater imaging system with the goal of lowering the technical and financial barriers to performing oceanographic research. SeeStar is a modular imaging system which can be deployed on practically any platform and is good to a depth of 1,500 meters. In 2016, the team will begin designing the third-generation SeeStar. This more capable version will add in the ability to interface standard oceanographic sensors such as CTDs, oxygen sensors, and pH probes. The intern will work with the team on the instrument interfacing and data-storage module. This will require both electrical hardware and software tasks, perfect for an embedded software engineering or an electrical engineering student.

Gene Massion
Autonomous Profiling Float: MBARI is developing an autonomous profiling float to address oceanographic research questions in the coastal regions of the world ocean. Some exposure to systematic software engineering techniques will be required along with competency in an object oriented programming environment. C# is ideal but Java, C++, or another similar language will be fine. The selected intern will also participate in at-sea, test tank, and lab testing and data analysis of the current profiling float prototypes.We have several projects very well suited for a summer internship including the following:

Development of an automated, closed-loop test fixture to rigorously test a complete profiling float in the lab. The test fixture will acquire engineering data from the float, calculate the float trajectory based on a dynamic model of float forces, and close the loop by generating a pressure signal similar to what the profiler would see in the ocean. This project will require an intern with some experience in dynamic modeling, control systems, and Matlab/Simulink.

Evaluation of commercially available nine-axis inertial measurement units to measure 3D float velocity. This project will require the ability to develop a model of IMU performance including noise and drift errors to calculate float velocity in 3 dimensions. This project will include automating a 3D translation stage to measure actual IMU performance for comparison against the model. Some experience with control systems and/or signal processing and Matlab/Simulink will be required.

Development of a comprehensive error detection and recovery framework for the profiling float. This project will build on the existing float error detection and recovery capability to develop a well-engineered, comprehensive capability to detect and respond to errors.

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 weekends. 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.

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.

Monique Messié
Physical/biological variability in Monterey Bay from AUV data: This project explores over 10 years of autonomous underwater vehicle (AUV) surveys in Monterey Bay. Data from AUV Dorado include physical measurements such as temperature and salinity, and biological measurements such as fluorescence and bioluminescence. The intern will work with oceanographic data and derived proxies (in particular proxies for autotrophic and heterotrophic plankton derived from fluorescence and bioluminescence) to generate products describing the physical/biological variability in Monterey Bay. This can include mean and climatological maps, as well as time series of seasonal and interannual variability. The method will be validated by comparing the Dorado products to satellite data for surface temperature and chlorophyll. While satellite data provide better surface coverage, Dorado provides information on vertical structure and heterotrophic communities. This project will thus advance our understanding of physical/biological variability in Monterey Bay and provide an unprecedented description of phyto and zooplankton communities in the bay. Preference will be given to applicants with experience in Matlab or R programming.

Tom O’Reilly and Brian Kieft
Wave Glider acoustic navigation: Our ocean communications “hot spot” uses a Wave Glider robot boat to communicate with, track, and follow underwater vehicles such as AUVs. This intern project will investigate how acoustic navigation techniques can be used to improve target tracking and following accuracy. Currently target location is up to approximately 50 meters due to various reasons, including unaccounted physical sensor offsets. Improving this accuracy will provide the opportunity for higher precision navigation of underwater assets. The project might also automate seafloor target location using the Wave Glider’s acoustic modem. Our current procedure logs acoustic target range along with Wave Glider latitude and longitude while flying “lawn mower” patterns over the estimated target location. We then perform a least squares fit to the data, to determine target latitude and longitude (i.e. the surface location where acoustic range is minimum). This procedure typically takes several hours of manual activity (e.g. issuing navigation commands, running the least squares fit). This project could develop software to automate the lawn mower pattern and least squares fit.

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 SchliningDuane Edgington, and Danelle Cline
Automated classification of deep-sea imagery: MBARI has a rich collection of underwater video and photographs, much 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.

Rich Schramm
ROV Ventana control-system software tools: This intern will work on one or more projects developing software for use with the remotely operated vehicle (ROV) Ventana. The intern may produce software modules and graphical user interfaces (GUIs) to test and control various ROV sub-systems or robotic toolsleds using yml markup or program in a high-level language such as Xojo, C++/Eclipse or Qt. Or they may develop and improve ROV pilot tools that log and play back the low-level vehicle control communications using Standard C or C++ and the LCM robotics messaging protocol. Candidates must have experience working in Linux at the command-line level, some experience writing or modifying software in a modern computer language (e.g., C/C++) with a terminal editor and/or some experience modifying and working with shell scripts and markup languages (eg. sh and yml).

Ken Smith, Crissy Huffard, and Linda Kuhnz
Climate change and deep-sea community structure: Using a 26-year time-series study at 4,000 meters depth in the eastern North Pacific, we have found significant changes in the overlying surface ocean processes related to food supply and benthic community responses at these abyssal depths. Time-series photographs taken hourly of the seafloor have shown major shifts in population densities and biomass amongst many dominant species of megafauna. Two species of holothurians (sea cucumbers) have shown the most 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 these two populations of holothurians over the past six months and, when compared with the earlier records, will analyze the entire temporal record with respect to ongoing changes in climate and upper-ocean processes determined from satellite monitoring.

Jordan Stanway and Carlos Rueda
Long-range AUV mission and data visualization: The Long Range AUV Group is looking for an intern to work on a human-computer interaction project. Since 2008 MBARI has invested significantly in the development of the long-range autonomous underwater vehicle (LRAUV), which fills a niche for weeklong, higher payload, biogeochemical surveys and field programs. The LRAUV’s software was designed to be extremely flexible and extensible to include new instruments. This flexibility comes with a cost. That cost is incurred anytime an end user wants to make a configuration change, mission change, or operational change to the vehicle. Currently there is no way for users to determine what a mission does without simulating the mission on a host machine. This is complicated and error prone, even for an expert user. While the existing interface provides some options for altering parameters in existing missions, they are non-graphical in nature and have proven to be error prone in the past with users entering incorrect values. The intern will be encouraged to work on a graphical mission preview and on historical LRAUV data to produce standard plots and videos for visualizing mission performance. The product of the internship will complement existing (Java/JavaScript) web applications, TethysDash and FleetStatus, as well as (Python/Matlab) analysis scripts and libraries (okeanidanalysi1s). The exact focus of the internship can be determined/revised depending on preference and background of the intern.

Susan von Thun and the video lab
Social Media: This project is ideal for an intern with experience in translating science and technology concepts into written and video content for the general public. The intern will work with MBARI staff, scientists, and engineers to develop stories about MBARI research. Responsibilities will include finding content within MBARI’s image and video archive and possibly from external sources to develop compelling stories about our research for MBARI’s social media outlets, including Facebook, Twitter, Instagram, and YouTube. The candidate must have experience in outreach and communication using social media, preferably with interests in science and technology. Skills in video editing, creating animated visuals, 3D illustrations, drawings, and information graphics are also desired, but not required. Applications may include writing samples and a portfolio in addition to the other required materials.

Alexandra Worden and Camille Poirier
Phytoplankton physiology: to be determined.

Matsumoto, G.I. 2015. A different approach to the research internship. Marine Technology Society. 49(4):35-44. DOI: 10.4031/MTSJ.49.4.1