Application procedure:
Applications for the MBARI 2009 Summer Internship Program are now being solicited. Applications should include a cover letter, a curriculum vitae, three letters of recommendation, and we would also like you to complete an online form. The cover letter should include a statement of your research interests (with specific mention of one of the following potential projects or areas), relevant coursework and grades, and complete contact details (home and work phone numbers and email address, if available). MBARI is an equal opportunity employer.
Below you will find 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 important part of your application and is essential in the application process. Please contact George Matsumoto if you have any questions. I have provided links to the mentors home pages (if available) so that you can learn more about the various mentors, please DO NOT contact the mentor directly.
Application materials (including letters) can be sent to MBARI via fax (831 775 1620), regular post, or by email. If you opt for an email application, please send your materials directly to George.
Science and technology illustration. It is often not possible to get good photos to illustrate many of our science and technology projects. Because of this, MBARI is seeking an intern with experience in translating science and technology concepts into visual media. It is likely that this intern would work on several different projects during the summer. Applications should include a portfolio (hard copy or digital) in addition to the other required material.
The Joseph Andrew Gashler Memorial Intern will participate in the development and testing of a new Autonomous Underwater Vehicle (AUV) designed for long ranges and endurances. AUVs are mobile robotic platforms which operate unattended by humans, and typically carry sensors for measuring ocean properties or mapping the seafloor. Our new vehicle, which we call Tethys, is designed to characterize the physical, chemical, and biological properties of the ocean up to 500 km from shore. Tethys must operate for weeks at a time without human intervention, beyond occasional satellite interactions. Such new AUVs are essential for understanding how changing climate effects.
The intern will work with the team of mechanical, electrical, and software engineers with extensive experience developing complex systems for ocean science. Depending on the skills of the extern, activities might include participating in tests designed to characterize aspects of the vehicle performance, or the development of software for demonstrating specific mission and control capabilities. This intern must be a student at the Moss Landing Marine Laboratories.
Francisco Chavez and Tim Pennington
Climate change and the greening of the California Current. After the 1997-98 El Nino, waters of Monterey Bay and central California have supported very high phytoplankton biomasses and productivities. Many of the drivers and dynamics of this change remain uncertain. We seek a student to explore the climactic causes and chemical and biological consequences of this change.
Danelle Cline and Duane Edgington
Automated visual event detection: Our project involves implementing a computer vision system that analyzes images collected by observatory cameras or underwater vehicles to detect, classify, and identify organisms. We are collaborating with labs at California Institute of Technology and University of Southern California to adapt and extend computer vision systems modeled after the human visual system. The internship involves working with a small team, participating in development, and analysis of still frames captured from a deep-water site in Monterey Bay. We welcome applicants with a background in computer science, machine vision, or marine biology. See our project web site AVED <http://www.mbari.org/AVED>.
Developing Ocean Observing Technologies on an Enterprise Service Bus (ESB): MBARI is collaborating with the National Center for Supercomputing Applications (NCSA) to prototype ocean observing technologies on the industrial software technology known as an Enterprise Service Bus (http://servicemix.apache.org/home.html). The intern will work with a team of MBARI software engineers to bring oceanographic instrumentation and its interactions onto the ESB. Development will be done in the Java programming language with potential tasks ranging from ESB component development to implementing an instrument control interface on an embedded controller. The end result of this work will provide MBARI and our collaborators with an interface to oceanographic instrumentation on an ESB to inform the international efforts developing software infrastructures for environmental science.
Zooplankton and Bioluminescence: Intern will work on a self-directed project involving bioluminescence, fluorescence, or phylogenetics of gelatinous zooplankton (ctenophores, siphonophores, or medusae). Molecular, chemical, or ecological projects may be possible. One high-priority project involves setting up a web site for monitoring coastal observations of jellyfish (and other animals). This would require programming with Drupal to interact with the Google Maps API.
Wave Energy for Vertical Profiling: This engineering intern project will support the development and testing of a device for collecting wave-energy on-board a profiling oceanographic instrument. A prototype of the system is being developed now and will be tested in the summer of 2009. Possible intern projects related to this effort include efficiency improvement of the system through lab testing, at-sea deployment of the prototype system, and analysis of system performance from data collected during test deployments.
Virtual 3D worlds: With increasing amounts of diverse oceanographic data being collected and archived new techniques are required to enable easier interpretation. The intern will develop data visualization tools to enable scientists and engineers to better understand experimental and natural processes encountered with MBARI's operations. We encourage highly motivated applicants with programming and video gaming experience to apply. Preference will be giving to applicants with skills in one of more of the following areas: script programming (Perl, Python, Ruby), 3D modeling tools (X3D, SketchUp), and an oceanography or engineering background.
Intern Logistical Coordinator: This intern will be assisting with the MBARI intern program. This assistance will likely include assisting the interns with travel logistics during the program as well as coordinating some educational activities on the weekends. It is expected that this intern will also be working on their own independent research project. The successful applicant will be an alumna/alumnus of the MBARI intern program and will stay in the same housing as the interns. Letters of recommendation are not required, but please elaborate on what your research project will entail in your application letter.
Education Intern: This intern would work with staff from both MBARI and our sister organization, the Monterey Bay Aquarium. This project would include closer integration and collaborations between the two institutions and should result in an integrated education and public awareness project that aligns well with the strategic plans of each organization. Applicants for this position should include some suggestions for what this project might entail.
Tom O'Reilly, Duane Edgington, and Kent Headley
Standard Instrument Protocols: The utility and cost-effectiveness of large-scale instrument networks are enhanced by instrument interoperability. Today's oceanographic instruments are characterized by very diverse non-standard software protocols; this diversity of protocols poses serious challenges to integration of large-scale interoperable sensor networks. Standard instrument protocols are now being developed to address these challenges, including the IEEE 1451 standards, OGC SWE, MBARI PUCK, and others. Working with a team of software engineers, the summer intern will explore one or more of these standard approaches. The intern may develop instrument "driver" software at the network level, or may develop software embedded in the instrument itself. The resulting interoperable instrumentation will first be tested in the laboratory, but later could be demonstrated on a deployed ocean observatory such as MARS or MOOS. See our project websites SENSORS (http://www.mbari.org/rd/sensors/sensors.htm), MARS (http://www.mbari.org/mars/), MOOS (http://www.mbari.org/moos/).
Onboard Autonomy: MBARI's Autonomous Systems group is engaged in research efforts to use advanced Artificial Intelligence (AI) techniques to enable Autonomous Underwater Vehicles (AUVs) to be more adaptive and contextually aware of their resource and goal commitments. Our onboard deliberative system T-REX (http://www.mbari.org/autonomy/TREX/ ) being used on an AUV platform (http://www.mbari.org/auv/), is based on the sense-deliberate-act paradigm synthesizing new mission plans in response to environmental conditions. T-REX uses a state-of-the-art temporal constraint-based planner developed originally at NASA Ames and flown on a number of space missions. Potential projects include:
1. PlanWorks debugging tool for EUROPA which allows us to leverage work done in visualization of constraint networks, token networks and timelines. The internship primarily be focused on developing PlanWorks to provide diagnostic information for T-REX.
2. Provide an intuitive science interface for mixed-initiative control of AUVs. The resulting code will need to visualize dynamic constraint networks underlying onboard and offboard plans for controlling an AUV asset at sea.
3. Interface an existing graphical AUV simulation toolkit with T-REX to provide a geographically ground post-facto visualization of T-REX from sea-trials.
4. Work on oversubscription resource modeling for T-REX. This will require understanding of the internals of T-REX modeling and constraint satisfaction for plan execution.
Highly motivated graduate or undergraduate students with substantial Java programming skills, C, or C++ programming skills, AI Planning and a background in Constraint Satisfaction would be a plus and are encouraged to apply.
Steve Ramp and Heather Kerkering
The Central and Northern California Ocean Observing System (CeNCOOS): The mission of CeNCOOS (see www.cencoos.org) is to integrate marine observations to inform decision makers and the general public. CeNCOOS produces information products to facilitate science-based management decisions affecting the health of the oceans. Topics of high interest presently include search and rescue, hazardous material spills, harmful algal blooms, coastal inundation, water quality, and marine protected area management. Summer interns are sought to help implement all aspects of the system including marine observations, data management and communications, operational ocean modeling and prediction, marine policy, education and outreach, and product development. Potential interns could have a scientific, marine policy, educational, or information technology inclination. The program is highly flexible and we can suggest specific projects which can be completed during the summer or potential interns may suggest projects of their own.
Midwater Ecology: Interns will have the opportunity to develop a project compatible with the lab's several ongoing research projects concerning mesopelagic and bathypelagic animals. Members of the lab group are currently working on the ecology, physiology, behavior and systematics of a number of midwater groups, including squids, crustaceans, fishes,and gelatinous zooplankton such as: polychaetes, medusae, siphonophores, ctenophores, larvaceans, and doliolids. Intern projects may involve using the ROV Ventana, 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.
Applications of Artificial Intelligence in Coastal Oceanography: MBARI is interested in combining advanced artificial intelligence (AI) and control techniques to advance observation of coastal waters using a range of robotic platforms. In collaboration with UCSC, we will deploy an autonomous surface vessel (ASV) for surface measurements of physical, chemical, and bio-optical properties relevant to understanding coastal "red tide" blooms. This joint biology-AI project is a collaboration of John Ryan and Kanna Rajan at MBARI, and Gabriel Elkaim at UCSC Engineering. The intern would:
1. test, deploy and maintain low-level control code for the ASV
2. install scientific instruments and interface them to the onboard controller
3. integrate a high-level AI-based controller designed at MBARI to drive decision-making onboard the ASV.
The above tasks will require testing the ASV in coastal Monterey Bay or in the nearby Elkhorn Slough. Additional details for decisional-level autonomy can be found at http://www.mbari.org/autonomy/TREX/. We invite applications from motivated graduate or undergraduate students. Substantial C or C++ programming experience is required. Background understanding of AI Planning and Constraint Satisfaction would be beneficial.
MBARI Deep Sea Guide: MBARI has a unique underwater video library cataloging the geologic features, organisms, and elements of MBARI research that occur within the Monterey Bay submarine canyon. We are currently seeking an individual to assist with the development of an on-line "Deep Sea Guide". The goals of the Deep Sea Guide are to create an encyclopedia describing the geology and biology of the Monterey Bay submarine canyon and to leverage video annotations cataloging the video features to present novel and valuable scientific information. The intern will work with a small team to develop a web- based interface to our existing databases. We encourage highly motivated applicants with web development or web design experience to apply. Preference will be giving to applicants with skills in one of more of the following areas: graphics design, Java or Groovy programming, web presentation technologies (AJAX, Flex, HTML+CSS, etc.), ocean sciences background.
Bentho-pelagic coupling: Our lab is studying the connections between climate variations, surface-water conditions, and deep-sea ecology at 4,100 m depth in the NE Pacific. Time-lapse and line-transect photography are used to evaluate the behavior, activity, body size, abundance, and distribution of animals on the abyssal seafloor at a long-term study site. There are currently image datasets from short and long-term time-lapse camera deployments, benthic camera-sled transects, as well as ROV and manned submersible photographic transects available for analysis. We are looking for an intern interested in utilizing such deep-sea photography to address ecological hypotheses, conduct comparisons of photographic techniques, or assist in transitioning from film-based to all-digital analytical methods. One or more days at sea collecting photographic data may also be possible during the internship.
Carbon Cycling in Marine Ecosystems: We study marine phytoplankton and how they interact with their environment. This involves work at sea as well as lab work, including flow cytometry and microscopy as well as whole genome sequencing, metagenomics and transcriptomics. Most of our work focuses on the smallest of the eukaryotic algae (less than 2 microns in size), but we also consider other microbial populations. In the long term we hope to gain a mechanistic understanding of how populations are controlled, both from the perspective of growth (nutrients, competition etc.) and predation. This internship opportunity is flexible in that we have a range of projects to be involved in, from purely computer based to "wet lab" work.