One of the Monterey Bay Aquarium Research Institute’s overarching goals is to transfer the knowledge gained, solutions devised, and technology developed to communities outside of MBARI. Our internal intellectual property committee offers guidance on technology transfer strategies. Basilio Martinez is the primary MBARI contact for technology transfer. He monitors incoming revenue, tracks payments to attorneys and the U.S. Patent and Copyright Office, and distributes royalties to MBARI and the inventors. The committee provides advice and patent information and negotiates licenses and commercialization support, working with advisors Evan Elder and Andrea Pesce at Stanford University’s Office of Technology Licensing.
MBARI uses a variety of strategies to transfer its developments to the greater community for public benefit. For example, some complex systems, such as the In Situ Ultraviolet Spectrophotometer, are licensed to commercial partners for manufacture and distribution to oceanographic researchers and resource managers. Some hardware and software systems, such as the Video Annotation and Reference System, are distributed for research use as open source software.
Some complex oceanographic systems developed at MBARI have been licensed and are commercially available:
In Situ Ultraviolet Spectrophotometer (ISUS)
Satlantic’s In Situ Ultraviolet Spectrophotometer (ISUS) V3 nitrate sensor (developed in Ken Johnson’s laboratory at MBARI) uses advanced ultraviolet absorption technology to accurately measure nitrate concentrations in aquatic environments in real time. Satlantic’s Deep SUNA, which is based on the ISUS sensor, was designed for integration into autonomous underwater vehicles.
Environmental sample processor (ESP)
McLane Research Laboratories manufactures and markets the Environmental Sample Processor (ESP) for in situ collection and analysis of seawater samples. This electromechanical, fluidics system (developed at MBARI under Chris Scholin’s leadership) can collect discrete water samples, concentrate microorganisms, plankton, or particles, and automate application of molecular probes in order to identify organisms and their gene products. The resulting data are available for remote retrieval and analysis in near-real time.
SeaFET ocean pH sensor
Satlantic has commercialized the SeaFET ocean pH sensor developed in Ken Johnson’s lab at MBARI in collaboration with Todd Martz’s lab at Scripps Institution of Oceanography. The instrument is an ion selective field effect transistor sensor for accurate long-term pH measurements in shallow ocean habitats.
Land/Ocean Biogeochemical Observatory
Land/Ocean Biogeochemical Observatory (LOBO) is a networked mooring system for continuous monitoring of complex cycles being commercialized by Satlantic. More info at: http://onlinelibrary.wiley.com/doi/10.4319/lom.2008.6.263/abstract.
New technology is currently available for licensing.
- MBARI’s high resolution pH electrode circuit board design for commercially available pH probes
MBARI has provided non-exclusive license agreements for a variety of oceanographic equipment design documentation for use in the exploration of the oceans to advance scientific knowledge:
Transportable remotely operated vehicle
MBARI’s Mini ROV is a portable, 1500-meter inspection class remotely operated vehicle that a small crew (one to two people) can operate off ships of opportunity around the world. The vehicle is capable of limited sampling, video transects, instrument deployments, and is outfitted with core instruments: camera, scanning sonar, lasers, LED lights, CTD, and bolt-on tool skids for mission-specific sampling. Read more at: MiniROVSystemSpecificationsADS.pdf.
Cable-laying and plowing toolsled
The cable-laying toolsled for remotely operated vehicles was developed to deploy fiber optic cable to interconnect deep-sea instrument clusters. The toolsled incorporates the capability to deploy five kilometers of fiber-optic cable at depths to 2,000 meters, monitor and control cable payout speed, and manipulate instrument packages at the platforms. The MBARI team also developed a plow attachment to the cable-laying toolsled to control the vehicle path along the seafloor and plow a shallow trough to bury the cable.
Pressure housing for various sensors
Custom syringe pump
Incubation tray for shipboard experiments on phytoplankton
Heated funnel sampler for sampling hydrates
Electronic module latch mechanism on cabled observatory
Science instrument interface modules
Self-triggering event detector
Benthic event detector
OASIS system software
Software infrastructure and application for MBARI ocean observing systems
Software infrastructure and application for MBARI ocean observing systems (SIAM) is maintained under GNU GPL v3 via google code. https://code.google.com/p/mbari-siam/source/browse/
Visual event detection and classification system
Some software and hardware systems designed and developed at MBARI are available through open source license agreements:
Shoreside data system (SSDS)
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Oceanographic decision support system
The oceanographic decision support system (ODSS) provides a platform for situational awareness, planning, observation, archiving and data analysis. MBARI’s interdisciplinary team of computer scientists, engineers, biologists and oceanographers has used the system extensively for oceanographic experiments. The novelty of the system lies in the targeted domain, its evolving functionalities that closely tracks how ocean scientists are seeing the evolution of the field experiments, and its actual use by engineers, scientists and marine operations staff.
Spatial temporal oceanographic query system
The spatial temporal oceanographic query system (STOQS) is a geospatial database software package designed for providing efficient access to in situ oceanographic measurement data. This efficient data access capability enables development of advanced visualization and analysis tools.
Video annotation and reference system (VARS)
The Video Annotation and Reference System (VARS) is a software interface and database system that provides tools for describing, cataloging, retrieving, and viewing the visual, descriptive, and quantitative data associated with MBARI’s deep-sea video archives. More info at: http://hohonuuli.github.io/vars/index.html.
Deep-Sea Guide (DSG)
MB-System for processing swath mapping data
MB-System (the MB stands for multibeam) is an open source software package for the processing and display of bathymetry and backscatter imagery data derived from multibeam, interferometry, and sidescan sonars. This software developed and supported by MBARI’s Dave Caress and Dale Chayes of Lamont-Doherty Earth Observatory is distributed freely (and for free) in the form of source code for Unix platforms.
TD_xxx matlab software
TD_xxx is a toolkit of matlab objects and functions to perform simulation of floating body motions in the time domain. The intent is that the code is extensible, giving the user a high level of control over new forces that impact the motions of one or more floating bodies, tethered or untethered to one another. All of the linearized wave-hydrodynamics is complete allowing the user to concentrate on adding problem specific behaviors to the system without having to program the relatively complicated wave-body interactions. TD_xxx matlab software is available under a BSD open source license (typical for matlab).
SeeStar underwater imaging system
SeeStar was designed as a less expensive, easily deployed ocean imaging system. It has three parts—a camera, a battery pack, and LED lights—each contained in its own pressure housing. The pressure housings are made of relatively inexpensive PVC pipe with plastic end caps. More info at: https://bitbucket.org/mbari/seestar.
A plug and work protocol for ocean observatories
A Plug and Work Discussion Group with MBARI participants helped to build community consensus on plug-and-work instruments for ocean observatories. The “PUCK” protocol is distributed by the Open Geospatial Consortium (OGC), an international consortium of over 520 companies, government agencies, and research institutions promoting publicly available interface standards. MBARI distributes the PUCK reference design kit (PRDK) on the MBARI web site with an open source license. https://www3.mbari.org/pw/