Marcus Christie

The Open Grid Computing Environments collaboration: Portlets and services for science gateways

We review the efforts of the Open Grid Computing Environments collaboration. By adopting a general three-tiered architecture based on common standards for portlets and Grid Web services, we can deliver numerous capabilities to science gateways from our diverse constituent efforts. In this paper, we discuss our support for standards-based Grid portlets using the Velocity development environment. Our Grid portlets are based on abstraction layers provided by the Java CoG kit, which hide the differences of different Grid toolkits. Sophisticated services are decoupled from the portal container using Web service strategies. We describe advance information, semantic data, collaboration, and science application services developed by our consortium. Copyright

Building Grid Portal Applications From a Web Service Component Architecture

This work describes an approach to building Grid applications based on the premise that users who wish to access and run these applications prefer to do so without becoming experts on Grid technology. We describe an application architecture based on wrapping user applications and application workflows as Web services and Web service resources. These services are visible to the users and to resource providers through a family of Grid portal components that can be used to configure, launch, and monitor complex applications in the scientific language of the end user. The applications in this model are instantiated by an application factory service. The layered design of the architecture makes it possible for an expert to configure an application factory service with a custom user interface client that may be dynamically loaded into the portal.

The LEAD Portal: a TeraGrid gateway and application service architecture: Research Articles

Web portals are one of the possible ways to access the remote computing resources offered by Grid environments. Since the emergence of the first middleware for the Grid, works have been conducted on delivering the functionality of Grid services on the Web. Many interesting Grid portal solutions have been designed help organize remote access to Grid resources and applications from within Web browsers. They are technically advanced and more and more widely used around the world, resulting in feedback from the community. Some of these user comments concern the flexibility and user-friendliness of the developed solutions. In this paper we present how we addressed the need for a flexible and user-friendly Grid portal environment within the PROGRESS project and how our approach facilitates the use of the Grid within Web portals. Copyright

The Open Grid Computing Environments collaboration: portlets and services for science gateways: Research Articles

Web portals are one of the possible ways to access the remote computing resources offered by Grid environments. Since the emergence of the first middleware for the Grid, works have been conducted on delivering the functionality of Grid services on the Web. Many interesting Grid portal solutions have been designed help organize remote access to Grid resources and applications from within Web browsers. They are technically advanced and more and more widely used around the world, resulting in feedback from the community. Some of these user comments concern the flexibility and user-friendliness of the developed solutions. In this paper we present how we addressed the need for a flexible and user-friendly Grid portal environment within the PROGRESS project and how our approach facilitates the use of the Grid within Web portals. Copyright

Programming Paradigms for Scientific Problem Solving Environments

Scientific problem solving environments (PSEs) are software platforms that allow a community of scientific users the ability to easily solve computational problems within a specific domain. They are designed to hide the details of general purpose programming by allowing the problem to be expressed, as much as possible, in the scientific language of the discipline. In many areas of science, the nature of computational problems has evolved from simple desktop calculations to complex, multidisciplinary activities that require the monitoring and analysis of remote data streams, database and web search and large ensembles of supercomputer-hosted simulations. In this paper we will look at the class of PSE that have evolved for these “Grid based” systems and we will consider the associated programming models they support. It will be argued that a hybrid of three standard models provides the right programming support to handle the majority of the applications of these PSEs.

Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata

The amount of DNA sequencing data has been exponentially growing during the past decade due to advances in sequencing technology. Processing and modeling large amounts of sequencing data can be computationally intractable for desktop computing platforms. High performance computing (HPC) resources offer advantages in terms of computing power, and can be a general solution to these problems. Using HPCs directly for computational needs requires skilled users who know their way around HPCs and acquiring such skills take time. Science gateways acts as the middle layer between users and HPCs, providing users with the resources to accomplish compute-intensive tasks without requiring specialized expertise. We developed a web-based computing platform for genome biologists by customizing the PHP Gateway for Airavata (PGA) framework that accesses publicly accessible HPC resources via Apache Airavata. This web computing platform takes advantage of the Extreme Science and Engineering Discovery Environment (XSEDE) which provides the resources for gateway development, including access to CPU, GPU, and storage resources. We used this platform to develop a gateway for the dREG algorithm, an online computing tool for finding functional regions in mammalian genomes using nascent RNA sequencing data. The dREG gateway provides its users a free, powerful and user-friendly GPU computing resource based on XSEDE, circumventing the need of specialized knowledge about installation, configuration, and execution on an HPC for biologists. The dREG gateway is available at: https://dREG.dnasequence.org/.

Supporting Science Gateways Using Apache Airavata and SciGaP Services

The Science Gateways Platform as a service (SciGaP.org) project provides a rapid development and stable hosting platform for a wide range of science gateways that focus on software as a service. Based on the open source Apache Airavata project, SciGaP services include user management, workflow execution management, computational experiment archiving and access, and sharing services that allow users to share results and other digital artifacts. SciGaP services are multi-tenanted, with clients accessing services through a well-defined, programming language-independent API. SciGaP services can be integrated into web, mobile, and desktop clients. To simplify development for new clients, SciGaP includes the PGA, a generic PHP-based gateway client for SciGaP services that also acts as a reference implementation of the API. Several example gateways using these services are summarized.

The CSBG - LSU Gateway: Web based Hosted Gateway for Computational System Biology Application Tools from Louisiana State University

Science gateways are identified as an effective way to publish and distribute software for research communities without the burden of learning HPC (High Performance Computer) systems. In the past, researchers were expected to have in-depth knowledge about using HPC systems for computations along with their respective science field in order to do effective research. Science gateways eliminate the need to learn HPC systems and allows the research communities to focus more on their science and let the gateway handle communicating with HPCs. In this poster we are presenting the science gateway project of CSBG (Computational System Biology Group - www.brylinski.org) of Department of Biological Sciences with Center for Computation & Technology at LSU (Louisiana State University). The gateway project was initiated in order to provide CSBG software tools as a service through a science gateway.

Apache Airavata Resource Allocation System: A Tool for Allocating Resources in Science Gateways

Science Gateways provide user environments and a set of supporting services that help researchers make effective and enhanced use of a diverse set of computing, storage, and related resources. In a software framework like Airavata, the distributed computing resources such as local clusters, supercomputers, computational grids, and computing clouds are shared among multiple researchers. Hence it requires an allocations process to track the demand for their resources, understand the scientific objectives of their users, and decide among competing needs when faced with user demand that is greater than the available resources can supply. We describe the design and a prototype implementation in this presentation.

Science Gateway Implementation at the University of South Dakota: Applications in Research and Education

Science Gateways are virtual environments that accelerate scientific discovery by enabling scientific communities to more easily and effectively utilize distributed computing and data resources. Successful Science Gateways provide access to sophisticated and powerful resources, while shielding their users from the underlying complexities. Here we present work completed by the University of South Dakota (USD) Research Computing Group in conjunction with the Science Gateways Community Institute (SGCI) [1] and Indiana University on setting up a Science Gateway to access USDs high-performance computing resources. These resources are now available to both faculty and students and allow ease of access and use of USDs distributed computing and data resources. The implementation of this gateway project has been multifaceted and has included placement of federated user login, user facilitation and outreach, and integration of USDs cyberinfrastructure resources. We present this project as an example for other research computing groups so that they may learn from our successes and the challenges that we have overcome in providing this user resource. Additionally, this project serves to exemplify the importance of creating a broad user base of research computing infrastructure through the development of alternative user interfaces such as Science Gateways.