Press Archive

SDSC Announces the Release of Gemstone Version 1.0

Advanced Grid Computing Environment Powers Molecular Science

Published 10/11/2006

The GEMSTONE project, Grid Enabled Molecular Science Through Online Networked Environments, has released Version 1.0 of the Gemstone environment, a rich client interface to an important set of grid-enabled computational chemistry and biochemistry tools. Downloads, screenshots, and tutorials are available at

Gemstone is a full end-to-end web services architecture for grid computing, including data management, remote job creation, and access to computational applications. It is being developed with support from the NSF National Middleware Initiative, and through collaborations between the San Diego Supercomputer Center (SDSC) at UCSD; the National Biomedical Computation Resource (NBCR) at UCSD; the University of Zurich ; the University of Texas , El Paso , and the Center for Theoretical Biological Physics.

Gemstone provides users with a multi-platform and rich environment to access applications hosted at SDSC and NBCR.

The current set of applications includes:

  • Adaptive Poisson-Boltzmann Solver (APBS)
  • The General Atomic and Molecular Electronic Structure System (GAMESS)
  • Automated Docking of Flexible Ligands to Macromolecules (Autodock)
  • Spanish Initiative for Electronic Simulations with Thousands of Atoms (Siesta)
  • Molecular rotation and preparations (MolPrep)

Also included are a number of utility applications such as Babel , PDB2PQR, and psize.

The applications and utilities are provided as web services that can be integrated into any client application. The service implementations use grid computing middleware and computational clusters to provide the execution environment for the applications. Currently, a grid testbed is available and will be scaled as needed. The services support strong typing using XMLSchema and can support integration of capabilities from molecular to macromolecular scales.

Additional applications are planned. Access to Autodock and Siesta services requires registration with NBCR's My WorkSphere portal, but most are available without registration for the time being as a service to the community.

To access the services, users download the Gemstone frontend, which is available for MacOSX, Linux, and Windows. The Gemstone frontend provides discovery of services, a rich GUI-based access to application parameters, and integration with the local desktop environment. Security for the system is provided through GAMA, a grid-based credential repository, and requires registration through the NBCR portal.

Additional tools are also available that complement the services and user interface, including:

  • Opal v1.0 library: a toolkit leveraged by Gemstone for automatically wrapping legacy applications with web services technology. Opal supports security and cluster integration.
  • Topaz v1.0-beta: a Mozilla Firefox extension that provides data management for GridFTP servers.

Collaborators include the NSF-supported SDSC at UCSD; the NIH-supported NBCR at UCSD; the University of Zurich ; the University of Texas , El Paso ; and the NSF-supported Center for Theoretical Biological Physics at UCSD.

More information on the supported Gemstone applications can be found at: