Incorporation of Middleware and Grid Technologies to Enhance Usability in Computational Chemistry Applications

Abstract

Abstract. High performance computing, storage, visualization, and database infrastructures are increasing in complexity as research moves towards grid-based computing, often pushing breakthrough computational capabilities beyond the reach of scientists due to the time needed to harness the infrastructure. Hiding the underlying complexity of networked resources becomes essential if scientists are to utilize these resources in a time-effective manner. There are a myriad of solutions that have been proposed, ranging from underlying grid glue, to fully integrated problem solving environments. In this work, we discuss a workflow management system that is fully integrated with emerging grid standards but can be dynamically reconfigured. Through defined XML schema to describe both resources and application codes and interfaces, careful implementation with emerging grid standards and user-friendly interfaces, a "pluggable" event-driven model is created where grid-enabled services can be composed to form more elaborate pipelines of information processing, simulation, and visual analysis.

Topaz: Extending Firefox to Accommodate the GridFTP Protocol

“…So, for example, a web portal may provide an interface for GridFTP, but the GridFTP protocol is used only between the web server and the GridFTP server: so called "last-mile" communication to the end user uses standard web-based uploading. In contrast to web-portals, our previous work with Gemstone [2,13] suggests and supports our general idea presented in [6] of extending the Mozilla core framework with grid computing capabilities in order to provide scientists with a truly integrated environment, from desktop or laptop to the backend grid services and applications. The Mozilla framework, being developed as an open-source project by the Mozilla Foundation, provides much of the necessary infrastructure to build rich end-user applications across a very wide range of platforms.…”

SOAs for scientific applications: Experiences and challenges

“…atomic to macro-molecular, molecular to cellular, tissue to organ). For instance, a user may wish to utilize the highly accurate quantum models to calculate atomic charges (24), but opt for the less accurate but significantly more computationally tractable classical molecular dynamics approach for determining protein-ligand docking (28). Each of these capabilities has been developed by independent developer communities over long periods of time sometimes decades and in some cases by different but related domain communities.…”

SOAs for Scientific Applications: Experiences and Challenges

“…atomic to macro-molecular, molecular to cellular, tissue to organ). For instance, a user may wish to utilize the highly accurate quantum models to calculate atomic charges (24), but opt for the less accurate but significantly more computationally tractable classical molecular dynamics approach for determining protein-ligand docking (28). Each of these capabilities has been developed by independent developer communities over long periods of time sometimes decades and in some cases by different but related domain communities.…”