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» Programming in Biomolecular Computation
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ESOP
2012
Springer
13 years 5 months ago
Generate, Test, and Aggregate - A Calculation-based Framework for Systematic Parallel Programming with MapReduce
Abstract. MapReduce, being inspired by the map and reduce primitives available in many functional languages, is the de facto standard for large scale data-intensive parallel progra...
Kento Emoto, Sebastian Fischer, Zhenjiang Hu
ISCA
2007
IEEE
196views Hardware» more  ISCA 2007»
15 years 4 months ago
Anton, a special-purpose machine for molecular dynamics simulation
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the ...
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Je...
CSB
2005
IEEE
210views Bioinformatics» more  CSB 2005»
15 years 3 months ago
Problem Solving Environment Approach to Integrating Diverse Biological Data Sources
Scientists face an ever-increasing challenge in investigating biological systems with high throughput experimental methods such as mass spectrometry and gene arrays because of the...
Eric G. Stephan, Kyle R. Klicker, Mudita Singhal, ...
ALMOB
2006
102views more  ALMOB 2006»
14 years 9 months ago
Mining, compressing and classifying with extensible motifs
Background: Motif patterns of maximal saturation emerged originally in contexts of pattern discovery in biomolecular sequences and have recently proven a valuable notion also in t...
Alberto Apostolico, Matteo Comin, Laxmi Parida
JCC
2006
110views more  JCC 2006»
14 years 9 months ago
Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm
: This article describes a method for solving the geometric closure problem for simplified models of nucleic acid structures by using the constant bond lengths approximation. The r...
Heinz Sklenar, Daniel Wüstner, Remo Rohs