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MPIPairwiseStatSig

Ankit Agrawal, Sanchit Misra, Daniel Honbo, Alok Choudhary
2010 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10  
it is much time consuming since it involves generating an empirical score distribution by aligning one sequence of the sequence-pair with N random shuffles of the other sequence.  ...  Distributing the most compute-intensive portions of the pairwise statistical significance estimation procedure across multiple processors has been shown to result in near-linear speed-ups for the application  ...  MPIPairwiseStatSig can also be used in conjunction with a fast database search program like BLAST to recover the homologs missed by BLAST. HPDC'10, June 20-25, 2010, Chicago, Illinois, USA.  ... 
doi:10.1145/1851476.1851545 dblp:conf/hpdc/AgrawalMHC10 fatcat:rax25xlicnhxfg7azjcfhsqnie

Modeling sequence and function similarity between proteins for protein functional annotation

Roger Higdon, Brenton Louie, Eugene Kolker
2010 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10  
This assumption is based on the binary concept of homology in that proteins are or not homologous.  ...  based on functional rather than homologous groupings.  ...  Funding: NIH (5R01 GM076680-02 and UO1 DK072473), NSF (DBI-0544757 and NSF-07140) and Seattle Children's Research Institute internal funds to Eugene Kolker.  ... 
doi:10.1145/1851476.1851548 pmid:25101328 pmcid:PMC4120521 dblp:conf/hpdc/HigdonLK10 fatcat:d3b5rakolzaovm33k6frwwiirq

Data parallelism in bioinformatics workflows using Hydra

Fábio Coutinho, Eduardo Ogasawara, Daniel de Oliveira, Vanessa Braganholo, Alexandre A. B. Lima, Alberto M. R. Dávila, Marta Mattoso
2010 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10  
However, most of current SWfMS still lack on supporting parallel executions in high performance computing (HPC) environments.  ...  Experimental results using workflows with BLAST show performance gains with the additional benefits of distributed provenance support.  ...  HPDC'10, June 20-25, 2010, Chicago, Illinois, USA. Copyright 2010 ACM 978-1-60558-942-8/10/06 ...$10.00.  ... 
doi:10.1145/1851476.1851550 dblp:conf/hpdc/CoutinhoOOBLDM10 fatcat:ah7sv7vvqva55ba37izwdofx2u

Cloud computing paradigms for pleasingly parallel biomedical applications

Thilina Gunarathne, Tak-Lon Wu, Judy Qiu, Geoffrey Fox
2010 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10  
We review and compare each of the frameworks and perform a comparative study among them based on performance, efficiency, cost and the usability.  ...  We analyze the variations in cost between the different platform choices (eg: EC2 instance types), highlighting the need to select the appropriate platform based on the nature of the computation.  ...  This work was made possible using the compute use grant provided by Amazon Web Service which is titled "Proof of concepts linking FutureGrid users to AWS".  ... 
doi:10.1145/1851476.1851544 dblp:conf/hpdc/GunarathneWQF10 fatcat:6fzi7lxe45cmdkg3elb2skrrjm

CUDA-based triangulations of convolution molecular surfaces

Sérgio Dias, Kuldeep Bora, Abel Gomes
2010 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10  
Fortunately, the massive computational power of the new generation of low-cost GPUs opens up an opportunity window to solve these problems: real-time performance and cheap computing commodities.  ...  Our triangulation algorithm for molecular surfaces is based on a multi-threaded, parallel version of the Marching Cubes (MC) algorithm.  ...  HPDC' 10 , 10 June 20-25, 2010, Chicago, Illinois, USA. Copyright 2010 ACM 978-1-60558-942-8/10/06 ...$10.00. Figure 2 : 2 CPU runtime performance. Figure 3 : 3 GPU runtime performance.  ... 
doi:10.1145/1851476.1851553 dblp:conf/hpdc/DiasBG10 fatcat:chkrgki3ljgxdjjzozsv5nbkda

BTWorld

Maciej Wojciechowski, Mihai Capotâ, Johan Pouwelse, Alexandru Iosup
2010 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10  
Second, by observing the state of these trackers, BTWorld obtains information about the performance, scalability, and reliability of BitTorrent.  ...  We demonstrate the viability of our architecture by deploying it in practice, to observe and analyze one week of operation of a large part of the global BitTorrent network-over 10 million swarms and tens  ...  '10, June 20-25, 2010, Chicago, Illinois, USA.  ... 
doi:10.1145/1851476.1851562 dblp:conf/hpdc/WojciechowskiCPI10 fatcat:55fsg636urdnlhrqbsjellf7ne