Choonhan Youn

GEONGrid portal: design and implementations

We have developed the GEONGrid system for coordinating and managing naturally distributed computing, data, and cluster resources on the cyberinfrastructure. Recently, since the use of Grid technology is still very complex for researchers and scientists, the area of Grid Portals has made excellent progress. The Grid portal system is an emerging open Grid computing environment that promises to provide users with uniform seamless access to remote computing and data resources by providing an easy to use interface to cover over the complexity of more sophisticated Grid technologies. In this paper, we present our initial efforts in the design and implementation of service components in the GEONGrid portal. These service components may be implemented as Web services that follow the conventions of service‐oriented architecture design. In this approach, service components are self‐contained, have a well‐defined programming interface defined in WSDL, and communicate using SOAP messaging. In building a GEONGrid portal, we also use a component‐based user interface design. Portlets provide the desired component model for user interfaces in the same way as Web services. Using this approach, which allows Grid portals to be built out of reusable components, has the obvious advantages of reusability and modularity. Copyright

Leveraging XSEDE HPC resources to address computational challenges with high-resolution topography data

Leveraging service-oriented architectures and taking advantage of the high-performance compute resources provided by XSEDE, we have developed standards-based web services to address the challenges associated with processing large volumes of high resolution topography data. These web services make results from community software packages and other cyberinfrastructure-based applications available to the wider earth sciences community via the OpenTopography Facility and the CyberGIS Gateway.

Design and implementation of services for a synthetic seismogram calculation tool on the grid

We have built user environments that simplify and provide interactive access to data, models, and compute resources as well as integrate various distributed computational services to study earthquake waveforms utilizing 3D models and compute resources within the Geosciences Network (GEONgrid) and national computational grids, such as TeraGrid. These data and computing services are implemented using a Web services approach and are incorporated in a service-based portal architecture. We then illustrate how these data, models, and services can be used to build distributed, interactive scientific applications.

The GEON service-oriented architecture for Earth Science applications

Abstract The Geosciences Network (GEON) project has been developing cyberinfrastructure for data sharing in the Earth Science community based on a service-oriented architecture. The layered architecture consists of Core, Middleware, and Applications services. Core services provide system-level functions (e.g. user authentication), Middleware services provide generic capabilities (e.g. catalog search), and Application services provide functions that users directly interact with, including applications that are specific to Earth Sciences. The GEON ‘service stack’ includes a standardized set of these services and the corresponding software modules. The GEON Portal provides Web-based access to these services via a set of portlets. This service-oriented approach has enabled GEON to expand to new partner sites and leverage GEON services for other projects. To facilitate interoperation in a distributed geoinformatics environment, GEON is focusing on standards for distributed search across federated catalogs.

Cyberinfrastructure for Observatory and Monitoring Networks: A Case Study from the TEAM Network

Environmental-monitoring and observatory networks currently operating or under development at the national, regional, and global scales have the potential to provide an unprecedented understanding of our natural environment and the threats that endanger it. The breadth of these networks, as well as advances in technology (e.g., from mobile devices to in situ sensors and multidimensional satellite sensor data), will result in larger volumes of data and more complex data sets than ever before. All of these networks require robust cyberinfrastructure to support their varying mission, governance, operational, and scientific objectives. In this article, we use the Tropical Ecology Assessment and Monitoring (TEAM) Network as a fully functional environmental-monitoring network case study to highlight the key cyberinfrastructure components and services that support the network. We provide valuable lessons from our experience building the TEAM Network cyberinfrastructure and suggest future improvements that have broad applicability for other observatory and monitoring networks.

TEAM Network: Building Web-based Data Access and Analysis Environments for Ecosystem Services

A team of ecologists, computer scientists, and engineers from Conservation International (CI) and San Diego Supercomputer Center at the University of California San Diego (SDSC, UCSD) has been collaborating over the past 3 years to develop cyberinfrastructure for the TEAM (Tropical Ecology, Assessment and Monitoring) Network of tropical forest field sites. The TEAM project provides real-time data to understand how tropical forest ecosystems are being impacted by global climate change and land cover change and to improve conservation decisions. A major objective of this project is to provide information and services on tropical forest data disseminated by TEAM sites within countries participating in the TEAM network. The cyberinfrastructure provides a pervasive computational ecosystem, integrating grid computing infrastructure with highperformance backend resources, data warehouses, sophisticated client applications, new instruments, and embedded sensors, thus enabling a new paradigm for monitoring, understanding, and managing ecological and environmental systems. This paper presents the TEAM data management, access, and analysis system that provides end-to-end solutions for sensor-based data and field observations collected at TEAM sites. Specifically, two major applications are presented, viz., the “Data Query and Download Application (DQA)” application, which allows users to navigate and download diverse TEAM datasets such as Tree and Liana Biodiversity, Terrestrial Vertebrate, Climate and Forest Carbon data using a Google Maps based interface; and, the “Forest Carbon Calculator (FCC)” application, which calculates tree biomass using equations for forests with different precipitation regimes, thereby predicting relationships between tree biomass, tree diameter and wood density to estimate the amount of above ground carbon in the forests.

Web-based simulating system for modeling earthquake seismic wavefields on the grid

We have developed the SYNSEIS (SYNthetic SEISmogram) tool within the GEON (GEOscience Network) project to enable efficient computations of synthetic seismic waveforms for research and education. SYNSEIS is built as a distributed system to support the calculation of synthetic seismograms in 2D/3D media. The underlying simulation software is a finite difference code, E3D, developed by LLNL (S. Larsen). This code is embedded within the SYNSEIS environment and used by our SYNSEIS tool to simulate seismic waveforms of either earthquakes or explosions at regional distances (<1000km). The SYNSEIS architecture is based around a Web service model. Especially, the computing Web services seamlessly access Grid computing resources by hiding the complexity of grid technologies. Even though the Grid computing is well-established in many computing communities, its use among domain scientists still is not trivial because of multiple levels of complexities encountered. We have also developed the grid-enabling E3D application code which takes our own dialect XML inputs that include geological models that are accessible through standard Web services. Also, the XML inputs for this application code contain structural geometries, source parameters, seismic velocity, density, attenuation values, number of time steps to compute, and number of stations. In this paper, we emphasize the development of a state-of-the-art web-based scientific computational environment. Our system can be used to promote an efficient and effective modeling environment to help scientists as well as educators in their daily activities and speed up the scientific discovery process.

The Problem Solving Environments of TeraGrid, Science Gateways, and the Intersection of the Two

Problem solving environments (PSEs) are increasingly important for scientific discovery. Todays most challenging problems often require multi-disciplinary teams, the ability to analyze very large amounts of data, and the need to rely on infrastructure built by others rather than reinventing solutions for each science team. The TeraGrid Science Gateways program recognizes these challenges and works with science teams to harness high-end resources that significantly extend a PSEs functionality.

Developing metadata services for grid enabling scientific applications

In a web-based scientific computing, the creation of parameter studies of scientific applications is required to conduct a large number of experiments through the dynamic graphic user interface, without paying the expense of great difficulty of use. The generated parameter spaces which include various problems are incorporated with the computation of the application in the computational environments on the grid. Simultaneously, for the grid-based computing, scientific applications are geographically distributed as the computing resources. In order to run a particular application on the certain site, we need a meaningful metadata model for applications as the adaptive application metadata service used by the job submission service. In this paper, we present how general XML approach and our design for the generation process of input parameters are deployed on the certain scientific application as the example and how application metadata is incorporated with the job submission service in SYNSEIS (SYNthetic SEISmogram generation) tool.

NMR cyberinfrastructure: Web-based virtual file system for managing distributed NMR data

A key aspect of data cyberinfrastructure is the middleware for managing distributed scientific data with services for organizing, publishing and preserving data entities in a collaborative, data sharing environment. In this paper, we describe a virtual web-based file system for managing NMR (Nuclear Magnetic Resonance) data from multiple, distributed NMR spectrometers across the campus of UC San Diego. The environment provides an authenticated, web-based, single point of entry for users to access their data from any of the NMR systems. An intuitive graphical user interface allows users to view, annotate, search, refresh, upload, and download their own data files or files belonging to a group, based on user privileges. We provide details of the system, including the design of the NMR Portal, the central NMR data repository, and the data harvesting process.