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PPOPP
2006
ACM
15 years 10 months ago
Performance characterization of molecular dynamics techniques for biomolecular simulations
Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations...
Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwa...
IPPS
2006
IEEE
15 years 10 months ago
Exploiting processing locality through paging configurations in multitasked reconfigurable systems
FPGA chips in reconfigurable computer systems are used as malleable coprocessors where components of a hardware library of functions can be configured as needed. As the number of ...
T. Taher, Tarek A. El-Ghazawi
BMCBI
2011
14 years 7 months ago
A user-friendly web portal for T-Coffee on supercomputers
Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is t...
Josep Rius Torrento, Fernando Cores, Francesc Sols...
HPDC
2005
IEEE
15 years 9 months ago
Recording and using provenance in a protein compressibility experiment
Very large scale computations are now becoming routinely used as a methodology to undertake scientific research. In this context, ‘provenance systems’ are regarded as the equ...
Paul T. Groth, Simon Miles, Weijian Fang, Sylvia C...
SCOPES
2004
Springer
15 years 9 months ago
An Integer Linear Programming Approach to Classify the Communication in Process Networks
New embedded signal processing architectures are emerging that are composed of loosely coupled heterogeneous components like CPUs or DSPs, specialized IP cores, reconfigurable uni...
Alexandru Turjan, Bart Kienhuis, Ed F. Deprettere