John J. Helly

A method for interoperable digital libraries and data repositories

Abstract Aside from the basic importance of metadata in documenting, the characteristics of data for reuse is the fundamental role it plays in the functioning of digital libraries and data repositories. Metadata provides both the content of the search catalogs and provides part of the basis for performing quality control on the source data. In this paper, we describe a method for a scalable and decentralized system of interoperable digital libraries and data repositories. The description includes transportable metadata format, a persistent naming convention for arbitrary digital objects and a protocol for the asynchronous distribution of metadata. We also include a description of an operational data repository based on these methods.

Controlled publication of digital scientific data

How to balance free and open access to scientific data with privileged access to new results by authors while protecting them from being scooped by competing interpretations of their own data.

Structural design for management and visualization of information for simulation models applied to a regional scale

A Modeling Applications System Integrative Framework (MASIF) was developed to facilitate regional-scale long-term simulations. MASIF links an array of existing visualization, analytical, and data management software to manage large volumes of model inputs and outputs as well as model execution to facilitate model development and analysis. Information from MASIF is shown in visual form, an approach that we believe is preferable for comprehending information contained in large datasets associated with models that simulate processes and patterns at regional scales. As an example, MASIF was used to manage and visualize daily simulations of maize growth, development, and yield from 1055 Midwestern locations in the United States.

The Effect of Temperature and Thermal Distribution on Glycolysis in Two Rockfish Species (Sebastes)

Studies on the effects of temperature on the activities of Embden-Meyerhof (EM) glycolysis, and the hexose monophosphate shunt (HMP) in fishes have dealt mainly with exotic and/or acclimated fishes. This study reports the effects of short-term reductions in temperature on EM and HMP activity in two closely related species of temperate fishes (Sebastes spp.) and its possible relation to the thermal distribution of the species. Thermal distribution data were collected by SCUBA for S. mystinus and S. serranoides in King Harbor, Redondo Beach, California, USA. Activities of the pathways were determined in liver-tissue studies, using glucose-14C and liquid scintillation techniques following the method of Hochachka (1968) with modifications. The data were analyzed by distribution-free methods. Tissue studies indicated HMP activity in both species at lowered temperature (5°C), but only in S. serranoides at 15°C. Results indicate that S. mystinus is capable of instantaneous temperature compensation, possibly related to its tendency to occupy cold waters.

Spatial characterization of the meltwater field from icebergs in the Weddell Sea

We describe the results from a spatial cyberinfrastructure developed to characterize the meltwater field around individual icebergs and integrate the results with regional- and global-scale data. During the course of the cyberinfrastructure development, it became clear that we were also building an integrated sampling planning capability across multidisciplinary teams that provided greater agility in allocating expedition resources resulting in new scientific insights. The cyberinfrastructure-enabled method is a complement to the conventional methods of hydrographic sampling in which the ship provides a static platform on a station-by-station basis. We adapted a sea-floor mapping method to more rapidly characterize the sea surface geophysically and biologically. By jointly analyzing the multisource, continuously sampled biological, chemical, and physical parameters, using Global Positioning System time as the data fusion key, this surface-mapping method enables us to examine the relationship between the meltwater field of the iceberg to the larger-scale marine ecosystem of the Southern Ocean. Through geospatial data fusion, we are able to combine very fine-scale maps of dynamic processes with more synoptic but lower-resolution data from satellite systems. Our results illustrate the importance of spatial cyberinfrastructure in the overall scientific enterprise and identify key interfaces and sources of error that require improved controls for the development of future Earth observing systems as we move into an era of peta- and exascale, data-intensive computing.

Collaborative Management of Natural Resources in San Diego Bay

This article presents the results of a three-year effort at applying information technology to the problem of collaborative natural resource management in San Diego Bay. As such, it represents an approach to integrated coastal zone management (ICZM). This effort resulted from a collaboration between the San Diego Supercomputer Center at the University of California, San Diego and the San Diego Bay Interagency Water Quality Panel for the purpose of (1) developing an environmental data repository to facilitate the acquisition and sharing of data and (2) the development of a visual model of the bay in support of the development of a comprehensive, coordinated management plan for San Diego Bay. It was determined from this study that information technology is an important and key component to ICZM but that sociopolitical factors may override the benefits of decision-support systems and should be considered at the outset of any project of this kind.This article presents the results of a three-year effort at applying information technology to the problem of collaborative natural resource management in San Diego Bay. As such, it represents an approach to integrated coastal zone management (ICZM). This effort resulted from a collaboration between the San Diego Supercomputer Center at the University of California, San Diego and the San Diego Bay Interagency Water Quality Panel for the purpose of (1) developing an environmental data repository to facilitate the acquisition and sharing of data and (2) the development of a visual model of the bay in support of the development of a comprehensive, coordinated management plan for San Diego Bay. It was determined from this study that information technology is an important and key component to ICZM but that sociopolitical factors may override the benefits of decision-support systems and should be considered at the outset of any project of this kind.

Development of a Hydrologic Information System for CUAHSI

A Hydrologic Information and Observing System (HIOS) is being designed and developed by a group of academic hydrologists and the San Diego SuperComputer Center. This is part of a research program supported by the National Science Foundation through the Consortium of Universities for the Advancement of Hydrologic Science, Inc (CUAHSI). HIOS components include a hydrologic observations database, a digital watershed which synthesizes the hydrologic observations with GIS, remote sensing and weather and climate data, and a hydrologic analysis and visualization component to quantify fluxes and flows of water and constituents through the phases of the hydrologic cycle for a watershed region. Digital products from all HIOS components are stored in a Hydrologic Digital Library. The Neuse basin in North Carolina is being used as the illustrative watershed for development

SIOExplorer: Digital Library Project

The newly launched SIOExplorer: Digital Library Project is a joint effort between oceanographers, librarians and computer scientists to integrate access to data, imagery and publications, using modern database technologies and metadata standards.

A framework for sea level rise vulnerability assessment for southwest U.S. military installations

We describe an analysis framework to determine military installation vulnerabilities under increases in local mean sea level as projected over the next century. The effort is in response to an increasing recognition of potential climate change ramifications for national security and recommendations that DoD conduct assessments of the impact on U.S. military installations of climate change. Results of the effort described here focus on development of a conceptual framework for sea level rise vulnerability assessment at coastal military installations in the southwest U.S. We introduce the vulnerability assessment in the context of a risk assessment paradigm that incorporates sources in the form of future sea level conditions, pathways of impact including inundation, flooding, erosion and intrusion, and a range of military installation specific receptors such as critical infrastructure and training areas. A unique aspect of the methodology is the capability to develop wave climate projections from GCM outputs and transform these to future wave conditions at specific coastal sites. Future sea level scenarios are considered in the context of installation sensitivity curves which reveal response thresholds specific to each installation, pathway and receptor. In the end, our goal is to provide a military-relevant framework for assessment of accelerated SLR vulnerability, and develop the best scientifically-based scenarios of waves, tides and storms and their implications for DoD installations in the southwestern U.S.

Multi-institution testbed for scalable digital archiving

The Scripps Institution of Oceanography (SIO) and the Woods Hole Oceanographic Institution (WHOI) have joined forces with the San Diego Supercomputer Center to build a testbed for multi-institutional archiving of shipboard and deep submergence vehicle data. Support has been provided by the Digital Archiving and Preservation program funded by NSF/CISE and the Library of Congress.