2017 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, and
  5. 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.

Nancy Barr
Web development/content creation: This intern will create web content highlighting MBARI research and technology, whether by gathering and synthesizing existing material or working with scientists and engineers to bring together new text, data, images, and video. A web development background may be helpful;  editorial and communications experience will prove most valuable. Familiarity with WordPress is preferred, but not required.

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 seawater and life in the deep sea. Recently we have begun an investigation of gelatinous animals in the deep-sea. They 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. In addition, we are making progress on a third generation laser Raman spectrometer for use in the deep-sea. This summer we will be completing developmental work and testing of the instrument. Measurements both in the laboratory, and in the deep sea, are in progress and the spectra reveal a wealth of information on these ancient life forms and a variety of other substances. In addition, we will be spending a week at sea on the RV Western Flyer to investigate a variety of targets located by the mapping AUV on the bottom of the Santa Cruz basin. We plan to interrogate a number of these targets with our second generation laser Raman spectrometer (DORISS2) to appraise their chemical status.

Francisco Chavez
Coastal upwelling and ocean acidification: The California Current System experiences a high degree of variability in parameters associated with ocean acidification, in part due to episodic coastal upwelling events. MBARI’s coastal observations have provided, and continue to provide, invaluable time-series measurements of physical, biological, and chemical oceanographic processes relevant to ocean acidification. This project will involve a combination of field work, data analyses, research and scientific writing, to characterize observations and to further the growing body of literature.

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.

Steve Haddock
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.

Rich Henthorn
AUV operations and data analysis: Although a variety of autonomous underwater vehicles (AUVs) are operated at MBARI, they have one common feature: each generates copious amounts of data. The objective of this internship is development of software tools that automate analysis of both the science and engineering data created during AUV missions. Additionally, we may investigate practical designs for tools that help streamline AUV preparation and component testing for operations. Preferred applicants will be engineering or marine science students with experience writing code (e.g., C/C++, Python, Ruby) and be comfortable using command-line terminal interfaces in a OSX or Linux environment. These projects may require involvement with AUV operations on MBARI vessels.

Brent Jones
Underwater communications: This project would investigate using a Radio-Frequency IDentification (RFID) system to communicate wireless

Chad Kecy and Thom Maughan
SeeStar open-source imaging: 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 to a depth of 1,500 meters. In 2016, the team has begun 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 electrical hardware and software tasks—perfect for an embedded-software engineering or an electrical engineering student.

Brian Kieft
Long-range AUV: We are looking for an applicant with some software engineering experience to work on application of set/drift navigation correction based on previous fix history when bottom-aided deduced reckoning is not available (e.g. in deep water).

Lonny Lundsten
Northeast Pacific catshark ecology: We propose using video annotations from MBARI’s video annotation reference system (VARS) to determine and compare spatial and habitat associations of three deep-sea catsharks found in the Northeast Pacific, between 48°N and 32°N latitude. The three study species include: Apristurus brunneusApristurus kampae,, and Parmaturus xaniurus. Using MBARI’s VARS database, the candidate will re-examine video data collected opportunistically from ROV surveys between the years 1989-2016. Geographic Information System (GIS) will used in combination with video analysis to determine how landscape ecology influences species distribution. Long-term studies examining the life history and distribution of deep sea catsharks through their range will provide essential life history data needed for management of these data-deficient species. The candidate should have expertise in elasmobranch biology and will gain experience with video analysis, GIS and other statistical analysis methods.

Severine Martini and Steve Haddock
Data visualization for science and technology: The objective of this internship is to convert complex scientific information into creative and accurate visual representations. The intern will work with the Biodiversity and Biooptics lab to analyze one of MBARI’s large datasets, depending on their interests: for example, transcriptome sequences, displaying traits in a phylogenetic context, jellyfish distribution data collected from jellywatch.org, bioluminescent properties, and behaviors, or biodiversity trends. Methods can include plot representations, in interactive web-application (Shiny-R), dynamic graphs, or map representations that synthesize data. The intern working on this project will work at the interface between biology, ecology, statistics, analysis, and communication for scientific purposes. A background in R software is required.

Gene Massion
Autonomous profiling float projects: 1) 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 Labview, Matlab/Simulink, Python, C# or a similar programming language; or 2) 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.  Some exposure to systematic software engineering techniques will be required along with competency in an object oriented programming environment.  C#, C++ or another object oriented language will be fine.

George Matsumoto
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.

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. Expertise and/or strong desire to program in Python and familiarity with modern web technology will help the intern be successful with this project.

Bruce Robison
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.

Brian SchliningDuane 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.

Ken Smith and Crissy Huffard
Climate change and deep-sea community structure: Using a 28-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. Species of holothurians (sea cucumbers) and echinoids (sea urchins) 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 megafauna populations over the past year when compared with the entire temporal record with respect to ongoing changes in climate and upper-ocean processes determined from satellite monitoring. This past year will be especially important during the significant El Niño event in 2015-2016.

Alexandra Worden and Ken Hoadley
Comparative cellular physiology of marine phytoplankton:  We are seeking a motivated intern to help ongoing work which aims to better understand the molecular underpinnings which govern cellular response to environmental change. Specifically, our focus is on the green algae lineage Prasinophyceae, an important primary producer within both coastal and open ocean systems. Our lab utilizes a muti-tiered approach to understand Prasinophyte behavior at the photo-physiological, molecular and genomic level. The intern will have the opportunity to help with a number of ongoing projects within the lab and gain hands-on experience with molecular and genomic techniques.


Data repository
Data policy
What is happening in Monterey Bay today?
Central and Northern California Ocean Observing System
Chemical data
Ocean float data
Slough data
Mooring ISUS measurements
M1 ISUS CTD Data Display
Southern Ocean Data
Mooring data
M1 Mooring Summary Data
M1 Asimet
M1 Download Info
M1 EMeter
M1 Fluorometer (CeNCOOS)
M1 GPS Location
Molecular and genomics data
ESP Web Portal
Seafloor mapping
Upper ocean data
Spatial Temporal Oceanographic Query System (STOQS) Data
Tide prediction
Image gallery
Video library
Previous seminars
David Packard Distinguished Lecturers
Research software
Video Annotation and Reference System
System Overview
Annotation Interface
Video Tape User Guide
Video File User Guide
Annotation Glossary
Query Interface
Basic User Guide
Advanced User Guide
Query Glossary
VARS Publications
Oceanographic Decision Support System
MB-System seafloor mapping software
MB-System Documentation
MB-System Announcements
MB-System Announcements (Archive)
How to Download and Install MB-System
MB-System Discussion Lists
MB-System FAQ
Matlab scripts: Linear regressions
Introduction to Model I and Model II linear regressions
A brief history of Model II regression analysis
Index of downloadable files
Summary of modifications
Regression rules of thumb
Results for Model I and Model II regressions
Graphs of the Model I and Model II regressions
Which regression: Model I or Model II?
Matlab scripts: Oceanographic calculations
Matlab scripts: Sound velocity
Visual Basic for Excel: Oceanographic calculations
Educational resources
MBARI Summer Internship Program
2017 MBARI Summer Internship Program
2017 Intern Projects and Mentors
Education and Research: Testing Hypotheses (EARTH)
EARTH workshops
2016—New Brunswick, NJ
2015—Newport, Oregon
2016 Satellite workshop—Pensacola, FL
2016 Satellite workshop—Beaufort, NC
EARTH resources
EARTH lesson plans
Lesson plans—published
Lesson plans—development
Lesson drafts—2015
Lesson drafts—2016 Pensacola
Center for Microbial Oceanography: Research and Education (C-MORE) Science Kits
Sample archive
Internship Papers (last five years)
2015 Intern papers
2014 Intern papers ‎ ‎
2013 Intern papers ‎ ‎
2012 Intern papers
2011 Intern papers