Fast parallel markov clustering in bioinformatics using massively parallel computing on GPU with CUDA and ELLPACK-R sparse format

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 3, 2012, Pages 679-692

  Bustamam, Alhadi ^a   Burrage, Kevin ^b   Hamilton, Nicholas A ^c  

^a UNIVERSITY OF INDONESIA   (Indonesia)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

bioinformatics; CUDA; ELLPACK R sparse format; GPU computing; graphs and networks; Markov clustering; parallelism and concurrency; performance evaluation; PPI networks; scalable parallel programming

Indexed keywords

CUDA; ELLPACK-R SPARSE FORMAT; GPU COMPUTING; GRAPHS AND NETWORKS; MARKOV CLUSTERING; PARALLELISM AND CONCURRENCY; PERFORMANCE EVALUATION;

CLUSTERING ALGORITHMS; CONTENT BASED RETRIEVAL; MATRIX ALGEBRA; PARALLEL ARCHITECTURES; PARALLEL PROGRAMMING;

BIOINFORMATICS;

ARTICLE; BIOLOGY; CLUSTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER SIMULATION; DNA MICROARRAY; METHODOLOGY; PROBABILITY;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; COMPUTER SIMULATION; MARKOV CHAINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 84859362943     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.68     Document Type: Article

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