Xiaorong Xiang

Agent-based scientific simulation

Natural organic matter (NOM) is a heterogeneous mixture of compounds affecting ecosystem function and drinking water treatment. An agent-based stochastic model simulates NOM transformations, allowing forward modeling of NOMs synthesis and degradation. Its use of Java and Web technologies makes the simulation model accessible to scientists worldwide.

A self manageable infrastructure for supporting Web-based simulations

We describe the design and implementation of a self-manageable multi-tiered infrastructure to support Web-based scientific simulations. This infrastructure demonstrates not only the successful integration of Web servers, simulation servers, database servers, reports servers, data warehousing and mining, but also the ability to achieve self manageability: self-configuring, self-healing, self-protecting and self-optimizing. A scientific simulation program, NOMSIM (Natural Organic Matter Simulator), is used to demonstrate the effectiveness of this infrastructure.

A semantic Web services enabled Web portal architecture

Web services technologies are emerging as a new approach for supporting e-science and e-engineering by providing access to heterogeneous computation resources and integration of distributed scientific applications. In this paper, we propose a Web portal architecture that enables end users to access the distributed application through the Web interface and to compose new tasks by integrating a set of high level Web services provided by portal developers. The portal design demonstrates that flexibility, reusability and interoperability can be provided for both end users and portal developers by using semantic Web services technologies.

Improving the Reuse of ScientificWorkflows and Their By-products

Most current practical methodologies and workflow systems for service composition and workflow creation in e-science pursue a semi-automatic way to allow users to discover and select appropriate services to include in a workflow based on semantic and conceptual service definitions. However, few of these approaches consider the potential for reuse: to share the knowledge gained during the service composition process and to reuse complete or partial of existing workflows. We believe that providing a capability for reuse of this knowledge and workflows could be an important component in a workflow system. In this paper, we present a methodology and an enhanced system design to facilitate the reuse of knowledge and workflows. It contains a hierarchical workflow structure representation, knowledge management and knowledge discovery components to capture and manage the reusable information in a system, and an approach for using a graph matching algorithm to discover similar workflows.

Web Portal and Markup Language for Collaborative Environmental Research

The main purpose of existing Web portals is to promote information sharing over the Internet. In this chapter we present the design and implementation of a science portal, the Natural Organic Matter research portal, which is not only for information sharing but also provides tools to allow scientists to share remote computational resources and do science on the Web. An XML-based Markup Language, NOML, is provided to build the XML-based Web components and facilitate Web services development in the future. This portal also consists of a set of online simulators with an intelligent interface for guiding simulation configuration and various electronic communication tools. The development of this portal takes advantage of the J2EE and Oracle database technologies.

A Service-Oriented Data Integration and Analysis Environment for In Silico Experiments and Bioinformatics Research

In this paper, we present a practical experiment of building a service-oriented system upon current Web services technologies and bioinformatics middleware. The system allows scientists to extract data from heterogeneous data sources and generate phylogenetic comparisons automatically. This can be difficult to accomplish using manual search tools since sequence data is rapidly accumulating. A Web-based environment enables scientists to more effectively define a task, perform the task at a desired time, monitor the execution status, and view the results. The first prototype of this system is being evaluated on a phylogenetic research application, Mother of Green (MoG). Our evaluation demonstrates that a service-oriented architecture can accelerate scientific research, increase research productivity, and provide a new approach to doing science. We also discuss issues in design and implementation of the system and identify our future research directions to enhance the system