The open source Free Ocean CO2 Enrichment (xFOCE) technology is a resource to enable the oceanographic community to study the long-term impacts of rising levels of CO2 in the world's ocean environment.The issue of worldwide ocean acidification (OA) is a well-established fact. The impact of this change on the organisms and ecosystem of the ocean is not well understood, and has become a focal point for scientific inquiry. Meanwhile OA research is transitioning from laboratory experiments to in situ experiments. The Monterey Bay Aquarium Research Institute (MBARI) has been at the forefront of in-situ OA research through the use of the Free Ocean CO2 Enrichment (FOCE) concept.FOCE uses fundamental concepts in OA research to conduct in-situ research in a stabilized, long term, user-defined pH environment. Stemming from its experience, MBARI has taken the initiative to develop xFOCE. The "x" in xFOCE denotes the multi-disciplinary nature of OA research, and refers to the many and varied environments for experimentation.xFOCE is intended to provide the OA community with resources to help address their specific needs. Economic realities have resulted in stiff competition for funding to conduct ocean acidification research and xFOCE helps by providing a free reference design, community advice and cost saving information. The expectation is that xFOCE will be a long-term repository of FOCE information for OA research.The xFOCE website is a community-driven repository for information such as suitable materials, experiment chamber fabrication techniques, chamber stabilization, sensor recommendations, software and applications, and numerous other tools to assist researchers with their OA work. Although MBARI is providing the initial framework for xFOCE, the intention is that the OA community will use the open source concept and contribute resources to enrich the OA community.

The Monterey Bay Aquarium Research Institute (MBARI) has a long history of developing state of the art underwater instruments to support its scientific research. Often these devices are one of a kind, highly engineered pieces of equipment. While MBARI has successfully transferred technology to outside organizations, this generally required extensive training and end users with a specialized skill set. Often times, these instruments require precise machining and come with a high financial price tag. This paper outlines an approach to developing lower cost, easy to use scientific modules that have wide applicability to the greater oceanographic community. With this approach, MBARI is seeking increase access to ocean technology for science. The devices covered in this paper grew out of the development of the exportable Free Ocean CO2 Enrichment (xFOCE) system. The core of this system is a series of modular building blocks which add design flexibility and ease of fabrication and maintenance. Two of the base building blocks are the Gateway Node and Sensor Node. The Gateway Node acts as a central computer which is able to control any underwater experiment. The Sensor Node acts as multi-port interface to a wide range of scientific instruments. Both nodes were designed to be open source, and thus modifiable by the end user.

The utility and cost-effectiveness of instrument networks are enhanced by instrument interoperability. Today's oceanographic instruments are characterized by very diverse non-standard software protocols and data formats. This diversity of protocols poses serious challenges to integration of large-scale sensor networks. Standard instrument protocols are now being developed to address these challenges. Some of these standards apply at the IP-network level and enable integration of existing "lower level" proprietary instrument protocols and software components. Other approaches are intended to be implemented by the instrument device itself. These native instrument protocol standards offer the possibility of more uniform and simpler system architectures. We compare these various approaches, describe how they can be combined with one another, and describe some prototypes that implement them.

MBARI's MOOS moored network is a state-of-the-art ocean observatory for interdisciplinary science, consisting of interconnected "host nodes" on the ocean surface, midwater, and seafloor. Each node can accommodate a wide variety of instruments. We describe some of the challenges posed by the system's functional requirements, and how those challenges are addressed by the design of the system's onboard hardware and software. Integration of diverse instruments and their protocols into the network poses major system integration and maintenance challenges, particularly in the areas of instrument installation and control, data retrieval, and data interpretation. All of these functions must be reliably performed in an often hostile environment on networked at-sea platforms that are generally power limited. We describe a distributed software architecture and implementation that addresses these challenges

Cabled observatories, such as MARS or the regional scale cabled observatory system planned for in the NSF Ocean Observatories Initiative (001), consist of many deployed instruments that communicate with human operators and shore-side data repositories. In addition, these deployed devices may actually communicate with one another, facilitating capabilities such as autonomous event response. These potentially complex interactions between multiple entities - human and machine - require that knowledge of the system configuration be available to participants. Users of instrument data require information - metadata - about the sensor that generated the data. Software that coordinates and controls instruments requires access to the software interfaces of those devices. "Manual configuration" has been used on small-scale systems, but in a network consisting of hundreds or thousands of instruments, the configuration challenge becomes critical. We propose to address the problem through automation of the configuration process, which will be achieved at several levels.Automated configuration will simplify the system operator's task of building and maintaining the observatory network. We describe a small, low-powered information storage device that we call a "instrument puck". When plugged into a suitable computer (lab workstation, deployed observing node), information can be written to or read from the puck. While an instrument is being prepared for initial integration into the observatory, a technician "loads" a puck with information necessary to configure the instrument within the observatory, and then physically attaches the puck to its instrument. Thereafter the attached puck always travels with its instrument, no matter where it is being installed in the observing network.The information loaded into the puck encompasses whatever is necessary to enable automatic configuration and system integration of the instrument when it is plugged into the observatory network, and any other information required by observatory policies. This information may include structured descriptions of the instrument's sensor and data characteristics (metadata). The information can also include actual software code that is retrieved from the puck and executed by an observatory node when the device is plugged in; this code could implement distributed instrument control and data retrieval interfaces, allowing network-wide access to the instrument functionality. We believe the puck concept to be a powerful one; a given instrument puck is configured just once, enabling automatic configuration of its instrument no matter where it is installed on the network thereafter.We also describe mechanisms by which an instrument and its puck can be "discovered" by the observatory network when the devices are plugged in. Several approaches are explored, with varying degrees of automation. We evaluate these approaches with special consideration to electrical and safety aspects of the undersea environment. Information and results from our prototyping efforts will also be presented.

The authors' goal is to greatly increase access to the Arctic Ocean by creating and demonstrating a safe and economical platform capable of basin-scale surveys. Specifically, they are developing an autonomous underwater vehicle (AUV) for Arctic research with unprecedented endurance, and the capability to relay data through the Ice to satellites. They provide a means of monitoring changes taking place in the Arctic Ocean and investigate its impact on global climate changes. The vehicle will also be capable of seafloor surveys throughout the Arctic basin. Such a capability is of national and global interest and importance.

The Environmental Sample Processor (ESP) instrument has been designed by the Monterey Bay Aquarium Research Institute (MBARI) for ocean sampling and monitoring. The ESP is an in situ sampling and processing device that enables near real-time detection of specific microorganisms through the application of molecular probes. The intended use of ESP is a 1 to 3 month deployment in 50 meters maximum depth for detection of harmful algal blooms. The authors present an overview of the software architecture deployed on the ESP instrument. The ESP software design is applied on two prototype instruments with similar mechanical design, but different control electronics. Presented in this work is the software architectural framework used that allows for controlled start up, shutdown, task and event handling in a concurrent software environment. They discuss how object-oriented design patterns such as the Adapter pattern are used to solve design problems and how testing improved reliability. A description and examples are given of the flexible ESP macro language that allows scientists to automate chemical processing steps. And finally, an algorithm for DNA probe array image registration and data extraction involving low-pass filtering, connected components, rotational translation, and component recognition and interpretation is presented

The MBARI Ocean Observing System (MOOS) will consist of networked observation platforms and sensors deployed over a wide geographic area, distributed throughout the oceanic water column. The network will utilize a variety of communication links, including optical fiber, microwave, packet radio, satellite, and acoustic, resulting in diversity of throughput, latency, and intermittence throughout the network. The network membership will be highly dynamic and unpredictable, as links go "up" and "down", and devices are added to and removed from the network. The sensors themselves will include a wide range of off-the-shelf instruments as will as novel devices developed at MBARI and elsewhere; sensor interface protocols will thus be very diverse, as there are currently no widely recognized standards. These aspects of the ocean observing system network present challenging software engineering problems. The authors review available "smart network" software technologies that address these problems, and evaluate their feasibility for their system. Addressing the diversity of sensors and protocols, they describe a device called a sensor puck, that could provide a universal interface between any sensor and the network, and that enables spontaneous configuration and operation when the sensor is plugged into the network.