2018 Projects and Mentors

Applications for 2018 will be accepted until February 21st, 2018 (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:

  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.


Jim Barry
Deep-Sea Ecology: We have active projects in the laboratory and field investigating the effects of climate-related changes in ocean conditions on marine animals. One major research area focuses on how coastal upwelling, both currently and in the future, may affect the survival, growth, and reproduction of red abalone, a key coastal species in California. A summer intern would be involved in laboratory studies of some aspect of the performance of abalone larvae or juveniles under various ocean conditions, simulated using our “Upwelling Simulator”.  It may also be possible to involve interns in deep-sea studies, including respiration measuremntes of deep-sea animals and studies of deep-sea corals.

Dave Caress
Software development: one of several possible smallish application development projects associated with MB-System. Any of these will result in source code included in a widely used open source software project.
Data processing: Identifying/sizing animals in combined lidar and stereo photography low altitude surveys. R/V Carson daytrips included.

Francisco Chavez
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.

Andrea Fassbender
Coastal Organic Alkalinity: Organic acids found in coastal marine environments (often originating from terrestrial sources) can contribute to the seawater total alkalinity. However, most of the computational tools we use to study ocean acidification and the marine carbonate system do not account for organic alkalinity, which means that this could present an important bias in our interpretation of coastal data. This project aims to assess the importance of organic alkalinity in Monterey Bay and nearby inland waters (Elkhorn Slough and Salinas River). The intern will analyze existing data, collect samples from small boats and an MBARI research vessel, and assist our lab in evaluating the relevance of this issue for local ocean acidification and carbon cycle research. Successful candidates will be familiar with a programming language (MATLAB or Python) that can be used to analyze data. Our goal is for the summer intern to gain field work and data analysis experience, with their results contributing to a publication in a peer-reviewed journal.

Kevin Gomes and Alana Sherman
Web Application Developer: The engineering group is seeking an intern to develop a web application from the ground up.  This project will develop infrastructure to enable engineers to communicate development progress to the institute.  The work will require integration of data from existing systems into newly developed models and data storage.  With mentorship, the intern will gain experience developing a full stack web application using the latest web frameworks.  Programming experience required, web experience desired.

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.

Ken Johnson, Tanya Maurer, and Josh Plant
Biogeochemical software development: Software to visualize/quality control chemical and biological data from aglobal array of profiling floats.  The Biogeochemical-Argo program  (www.biogeochemical-argo.org) is a program to instrument the global ocean  with chemical and biological sensors.  Much of the US effort is hosted at MBARI.  We are looking for interns interested in developing software to use in the quality control and data visualization process.

Kakani Katija
Bioengineering: 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.

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).

Linda Kuhnz
Deep-Sea Corals: Ongoing studies of deep-sea corals provide important information about the role these animals play within the biological communities they inhabit. Size, age and growth, and predation are some of the parameters that can be assessed. This intern project involves evaluating various characteristics of corals using video obtained using the remotely operated vehicle Doc Ricketts. 

Gene Massion
Autonomous profiling float projects: The MBARI Chemical sensor lab is developing a profiling float designed to better understand the health of the ocean in the coastal zone.  We have a range of challenging projects that would be very suitable for a summer internship.  These include a) developing a more automated approach to the mission control and data analysis elements of our at-sea missions, b), improving the current depth and velocity control algorithms or c) improving the manufacturability and reducing the cost of the current design.  A background in one or more of the following areas will be required; data analysis using Matlab, software development using C#, control system design and development, mechanical design using Solidworks.

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.

Henry Ruhl and Alex Harper
Data Analysis/Web development/communications: CeNCOOS is seeking an intern to synthesize marine science and monitoring results from central California in support of coastal stakeholders. Experience in scientific analysis and communications, and social media is desired.  Experience with content management systems is preferred.  The intern will gain experience analyzing and 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.

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 Schlining
Software Applications for MBARI’s Media Management: MBARI has an extensive archive of nearly 30 years of underwater video that has been carefully annotated and curated. We are seeking an intern to develop new software applications to support the analysis, management, and access to this trove of scientifically valuable data. There are a number of possible applications for interns: develop web services for querying annotations and displaying video, create web-front ends for video and annotation access, or development of operating-system specific video players that integrate with MBARI’s annotation system. Applicants should have a background in software development or computer science.

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 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. 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 6 months and when compared with the earlier records, will analyze the entire temporal record to on-going changes in climate and upper ocean processes determined from satellite monitoring.

Yui Takeshita
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.

Alexandra Worden and Ken Hoadley
Ecology and dynamics of marine phytoplankton and their predators: – This intern will join the Worden lab to study algae using molecular methods or physiological studies to try to better understand how their diversity connects to ecosystem function

Products

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
Southern Ocean Data
Mooring data
M1 Mooring Summary Data
M1 ADCP (CeNCOOS)
M1 Asimet
M1 Download Info
M1 EMeter
M1 Fluorometer (CeNCOOS)
Molecular and genomics data
ESP Web Portal
Seafloor mapping
Upper ocean data
Spatial Temporal Oceanographic Query System (STOQS) Data
Image gallery
Video library
Seminars
Previous seminars
David Packard Distinguished Lecturers
Research software
Video Annotation and Reference System
System Overview
Knowledgebase
Annotation Interface
Video Tape User Guide
Video File User Guide
Annotation Glossary
Query Interface
Basic User Guide
Advanced User Guide
Results
Query Glossary
FAQ
VARS Publications
Oceanographic Decision Support System
MB-System seafloor mapping software
How to Download and Install MB-System
MB-System Documentation
MB-System Announcements
MB-System Announcements (Archive)
MB-System FAQ
MB-System Discussion Lists
MB-System YouTube Tutorials
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 Summer Interns Blog
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
Adopt-A-Float Program
Center for Microbial Oceanography: Research and Education (C-MORE) Science Kits
Publications
Sample archive
Internship Papers (last five years)
2017 Intern papers
2016 Intern papers
2015 Intern papers ‎ ‎
2014 Intern papers ‎ ‎
2013 Intern papers