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SPICE

SPICE

SPICE wins the HPC Analytics Challenge Award at SC|05

SPICE-Simulated Pore Interactive Computing Environment: Using Grid computing to understand DNA translocation across protein nanopores

SPICE is part of a joint UK/US high-end computing project funded by the EPSRC (grant EP/D500028/1) and the US National Science Foundation (NSF) that used sophisticated grid infrastruture- comprised of an integrated Web Services (WS) based steering and hosting environment, along with advanced networking capabilities to effectively utilise the computational resources of a federated Transtlantic Grid. Designed to facilitate novel analysis techniques, the scientific aim of the project is to advance the understanding of the vital translocation process of nucleic acids (DNA) across membrane channel pores in biological cells.

SPICE exploits high performance resources on adminstratively-distinct Grids -the UK's National Grid Service (NGS) and the US's TeraGrid to form a single federated Grid. The UK's high bandwidth optical network UKLight, within the ESLEA Project, provides a semi-persistent link between the resources on the trans-Atlantic Grid.

SPICE has been showcased at the UK e-Science All Hands Meeting 2005, at iGrid 2005 and at SC|05.

During SC|05, three groups worked on a shared Transatlantic Federated Grid. All three projects - NekTAR (led by George Karniadakis, Brown University), VORTONICS (led by Bruce Boghosian, Tufts University) and SPICE (led by Peter Coveney, University of London) - grappled with challenging large-scale research problems that require grid computing to be solved. For more information about these projects see the press release hosted on the TeraGrid website.

SPICE has won the HPC Analytics Challenge Award at Super Computing 2005

The HPC Analytics Challenge is an award competition honoring select technical and commercial applications that use leading-edge analytics techniques to solve complex, real-world problems. The growing need to leverage large amounts of underutilized data has led to the use of sophisticated methods for analysis and high-end visualization in conjunction with high performance computing, bandwidth and networking capabilities. The HPC Analytics Challenge is a unique opportunity for researchers, engineers and analysts to showcase innovative techniques of rigorous data analysis (forecasting, data mining, optimization, predictive analysis) and high-end visualization (dynamic modeling, real-time rendering).

The EPSRC press release on SPICE at SC|05 is available here.

SPICE SC|05 double sided flyer is available here.

A demonstration video can be seen here.

SPICE has won the ISC Life Sciences Award at International Supercomputer Conference 2006

The EPSRC and NSF funded SPICE project has won the ISC Life Sciences Award for 2006.

The award-winning paper is available here.

Publications

  • S. Jha, P. V. Coveney and M. J. Harvey, "SPICE: Simulated Pore Interactive Computing Environment", Proceedings of the 2005 ACM/IEEE Conference on Supercomputing, (2005). Available here (pdf) or from the ACM Portal here.
  • S. Jha, M. J. Harvey, P. V. Coveney, N. Pezzi, S. Pickles, R. Pinning and P. Clarke, "SPICE: Simulated Pore Interactive Computing Environment - Using Grid computing to understand DNA translocation across protein nanopores embedded in lipid membranes", UK e-Science All Hands Meeting 2005. Available here.
  • S. Jha, S. Wan,and P.V. Coveney, "Computing free energies for `real' systems using molecular dynamics simulations", Capability Computing, the Newsletter of the HPCx community, 6, 8-10, (2005). Available here.
  • B.M. Boghosian, P.V. Coveney, S. Dong, L.I. Finn, S. Jha, G. Karniadakis and N. Karonis, "Nektar, SPICE and Vortonics: Using Federated Grids for Large Scale Scientific Applications", (2006). Available here.
  • S. Jha, P.V. Coveney and M. J. Harvey, 'SPICE: Simulated Pore Interactive Computing Environment - Using Federated Grids for "Grand Challenge" Biomolecular Simulations', International Supercomputer Conference 2006. Available here.

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