Software and the Concurrency Revolution
Queue - Multiprocessors
Queue - GPU Computing
Queue - GPU Computing
Scalable Parallel Programming with CUDA
Queue - GPU Computing
Bioinformatics
Graph Clustering Via a Discrete Uncoupling Process
SIAM Journal on Matrix Analysis and Applications
Many-core algorithms for statistical phylogenetics
Bioinformatics
Challenges and opportunities of obtaining performance from multi-core CPUs and many-core GPUs
ICASSP '09 Proceedings of the 2009 IEEE International Conference on Acoustics, Speech and Signal Processing
MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA
ASAP '09 Proceedings of the 2009 20th IEEE International Conference on Application-specific Systems, Architectures and Processors
IEEE Micro
Programming Massively Parallel Processors: A Hands-on Approach
Programming Massively Parallel Processors: A Hands-on Approach
Bio-sequence database scanning on a GPU
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Improving the Performance of the Sparse Matrix Vector Product with GPUs
CIT '10 Proceedings of the 2010 10th IEEE International Conference on Computer and Information Technology
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Markov clustering (MCL) is becoming a key algorithm within bioinformatics for determining clusters in networks. However, with increasing vast amount of data on biological networks, performance and scalability issues are becoming a critical limiting factor in applications. Meanwhile, GPU computing, which uses CUDA tool for implementing a massively parallel computing environment in the GPU card, is becoming a very powerful, efficient, and low-cost option to achieve substantial performance gains over CPU approaches. The use of on-chip memory on the GPU is efficiently lowering the latency time, thus, circumventing a major issue in other parallel computing environments, such as MPI. We introduce a very fast Markov clustering algorithm using CUDA (CUDA-MCL) to perform parallel sparse matrix-matrix computations and parallel sparse Markov matrix normalizations, which are at the heart of MCL. We utilized ELLPACK-R sparse format to allow the effective and fine-grain massively parallel processing to cope with the sparse nature of interaction networks data sets in bioinformatics applications. As the results show, CUDA-MCL is significantly faster than the original MCL running on CPU. Thus, large-scale parallel computation on off-the-shelf desktop-machines, that were previously only possible on supercomputing architectures, can significantly change the way bioinformaticians and biologists deal with their data.