Gemstone version 1.0 released

Submitted by ksb on Mon, 10/02/2006 - 00:00.
::

The GEMSTONE project announces the release of Version 1.0 of the
Gemstone environment, a rich client interface to a set of grid-
enabled computational chemistry and biochemistry tools. Downloads,
screenshots and tutorials are available at:

http://gemstone.mozdev.org

Gemstone provides users with a multi-platform and rich environment to
access the applications currently hosted at the San Diego
Supercomputer Center (SDSC) and the National Biomedical Computation
Resource (NBCR).

The current set of applications include:

  • 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 various 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
services to the community.

To access the services users should download the Gemstone frontend
available for MacOSX, Linux or Windows. The Gemstone frontend
provides discovery of services, a rich GUI-based access to
application parameters, and integration with the local desktop
environment. The 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.

Gemstone represents 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
through a grant from NSF National Middleware Initiative
(SCI-0438430), and through collaborations between SDSC, NBCR, the
University of Zurich, University of Texas, El Paso, and the Center
for Theoretical Biological Physics.

Links:

Please contact Kim Baldridge (kimb@sdsc.edu) or Karan Bhatia
(karan@sdsc.edu)
for any questions.