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» Reconfigurable Molecular Dynamics Simulator
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FCCM
2006
IEEE
133views VLSI» more  FCCM 2006»
14 years 3 months ago
A Scalable FPGA-based Multiprocessor
It has been shown that a small number of FPGAs can significantly accelerate certain computing tasks by up to two or three orders of magnitude. However, particularly intensive lar...
Arun Patel, Christopher A. Madill, Manuel Salda&nt...
BMCBI
2010
149views more  BMCBI 2010»
13 years 10 months ago
RuleMonkey: software for stochastic simulation of rule-based models
Background: The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be...
Joshua Colvin, Michael I. Monine, Ryan N. Gutenkun...
BMCBI
2006
179views more  BMCBI 2006»
13 years 10 months ago
Multiscale Hy3S: Hybrid stochastic simulation for supercomputers
Background: Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuation...
Howard Salis, Vassilios Sotiropoulos, Yiannis N. K...
MABS
2007
Springer
14 years 4 months ago
Middleware Support for Performance Improvement of MABS Applications in the Grid Environment
The Grid can be the right environment for large-scale Multi-agent based simulation (MABS) applications. However, due to the nature of the Grid and the characteristics of MABS, achi...
Dawit Mengistu, Paul Davidsson, Lars Lundberg
ISMB
1994
13 years 11 months ago
An Efficient Method for Multiple Sequence Alignment
Multiple sequence alignment has been a useful methodin the study of molecular evolution and sequence-structure relationships. This paper presents a newmethodfor multiple sequence ...
Jin Kim, Sakti Pramanik