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Distributed Sequence Alignment Applications for the Public Computing Architecture

S. Pellicer, Guihai Chen, K.C.C. Chan, Yi Pan
2008 IEEE Transactions on Nanobioscience  
BLAST.  ...  Our implementation of these two problems on the Berkeley open infrastructure for network computing (BOINC) platform demonstrates a runtime reduction factor of 1.15 for sequence alignment and 16.76 for  ...  The contrast between these two cluster implementations points out two issues with data parallel BLAST implementations.  ... 
doi:10.1109/tnb.2008.2000148 pmid:18334454 fatcat:cayuubjz2jbwrhjknxdkm6nguq

Parallelization of local BLAST service on workstation clusters

R.C Braun, K.T Pedretti, T.L Casavant, T.E Scheetz, C.L Birkett, C.A Roberts
2001 Future generations computer systems  
These developments will demand ever more efficient means of BLASTing sets of data that will make single processor implementation on powerful workstations infeasible.  ...  This basic comparison operation, usually carried out by the well-known BLAST program on one subject sequence against the internationally available databases of nearly five million target sequences, is  ...  Some compute nodes in the current cluster of workstations have several CPUs and therefore can handle more than one simultaneous BLAST job.  ... 
doi:10.1016/s0167-739x(00)00057-1 fatcat:6dvwzv7zbzglbnklevkkmidifm

A Survey of Multiple Sequence Alignment Parallel Tools

MohammedW. Aly, NaglaaM. Reda, KasimA. Alsalem, FayedF.M. Ghaleb
2016 International Journal of Advanced Research  
Second it creates a guide tree constructed from pair-wise sequence distances using a clustering method such as UPGMA [15] or Neighbor-Joining [16] .  ...  The performance of each tool depends on the  ...  The algorithm has been implemented on a cluster of workstation on 16 node using MPI library.  ... 
doi:10.21474/ijar01/382 fatcat:lrxb5u5mkfcsthnrwfrxcfly6a

XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data

Daniel N Frank
2008 BMC Bioinformatics  
Clusters can be assembled based on furthest-, mean-, or nearest-neighbor rules.  ...  OTU clustering is implemented through the program sortx, which was written in tandem with XplorSeq (Fig. 6F ).  ... 
doi:10.1186/1471-2105-9-420 pmid:18840282 pmcid:PMC2577119 fatcat:uvhw2xgpunbbjbjjwxevaoxnxu

Trellis driver: distributing a java workflow across a network of workstations

N. Lamb, P. Lu, A. Fyshe
2004 Workshops on Mobile and Wireless Networking/High Performance Scientific, Engineering Computing/Network Design and Architecture/Optical Networks Control and Management/Ad Hoc and Sensor Networks/Compil  
We describe the design and implementation of the Trellis Driver, a newly-developed Java module that runs jobs using TrellisDriver.exec() and allows jobs to be scheduled across clusters and metacomputers  ...  Specifically, we use a cluster of workstations as the hardware platform.  ...  Thus, PA could theoretically issue many calls to Runtime.exec() and start multiple Blast jobs in parallel, and later call Process.waitFor() on each process to verify its outcome.  ... 
doi:10.1109/icppw.2004.1328018 dblp:conf/icppw/LambLF04 fatcat:7dn5yt66fbdwtp2xndnzxwsvea

TurboBLAST : a parallel implementation of blast built on the turbohub

R.D. Bjornson, A.H. Sherman, S.B. Weston, N. Willard, J. Wing
2002 Proceedings 16th International Parallel and Distributed Processing Symposium  
This paper describes TurboBLAST, a parallel implementation of BLAST suitable for execution on networked clusters of heterogeneous PCs, workstations, or Macintosh computers.  ...  BLAST (Basic Local Alignment Search Tool) is by far the most widely used application for rapid screening of large sequence databases.  ...  In this case, the benchmarks were run on an IBM Linux cluster containing 8 dualprocessor workstations connected via 100-Megabit Ethernet.  ... 
doi:10.1109/ipdps.2002.1016583 dblp:conf/ipps/BjornsonSWWW02 fatcat:v6hvhmsccjf3rggwy3huntk4m4

Multi-granularity Parallel Computing in a Genome-Scale Molecular Evolution Application [chapter]

Jesse D. Walters, Thomas B. Bair, Terry A. Braun, Todd E. Scheetz, John P. Robinson, Thomas L. Casavant
2009 Lecture Notes in Computer Science  
Very high degrees of parallelism (up to 65x speedup on 4,096 processors) were reported, yet the overall execution time for a realistic problem size was still on the order of 12 days.  ...  In addition to benchmarking results that show up to 80% speedup efficiency on 8 CPU cores, we report on the biological accuracy and relevance of our results compared to a reported set of known xenologs  ...  Table 3 shows the results of parallelization of UIPTC on a set of HP workstations with dualcore Opteron processors. For small numbers of CPUs, almost linear speedup is observed.  ... 
doi:10.1007/978-3-642-03275-2_6 pmid:21841894 pmcid:PMC3155254 fatcat:5pegqqlapna3hkecunkr6rvbcy

Improving the Research Environment of High Performance Computing for Non-cluster Experts Based on Knoppix Instant Computing Technology [chapter]

Fumikazu Konishi, Manabu Ishii, Shingo Ohki, Yusuke Hamano, Shuichi Fukuda, Akihiko Konagaya
2006 Lecture Notes in Computer Science  
One challenge in the instant computing area is constructing a cluster system instantly, and then readily restoring it to its former state.  ...  We have designed and implemented a new portable system that can rapidly construct a computer environment where highthroughput research applications can be performed instantly.  ...  Our work represents the first step in exploring design and implementation issues regarding instant computing technology.  ... 
doi:10.1007/11823285_123 fatcat:pbnumjrhx5h25buucawpe2yqou

GeneRAGE: a robust algorithm for sequence clustering and domain detection

A. J. Enright, C. A. Ouzounis
2000 Bioinformatics  
Initial clusters containing multi-domain families, are split into their constituent clusters using the information obtained by the multidomain detection step.  ...  This algorithm can hence quickly and accurately cluster large protein datasets into families.  ...  Patent application filed on behalf of EMBL.  ... 
doi:10.1093/bioinformatics/16.5.451 pmid:10871267 fatcat:ipotocxuxvcnlcae7vbxb5tzum

Dynamite-blasting obstacles to parallel cluster computing [chapter]

G. D. van Albada, J. Clinckemaillie, A. H. L. Emmen, J. Gehring, O. Heinz, F. van der Linden, B. J. Overeinder, A. Reinefeld, P. M. A. Sloot
1999 Lecture Notes in Computer Science  
Workstations make up a very large fraction of the total available computing capacity in many organisations.  ...  Pilot versions of the checkpointer and migrator were implemented for the SUN Solaris operating system, and have been tested on OS versions 2.5.1 and 2.6 on UltraSparc workstations.  ...  As a result, the application uses the whole workstation cluster efficiently and expensive compute time is not wasted migrating single tasks one at a time.  ... 
doi:10.1007/bfb0100591 fatcat:knpxd5rktnd2xl6eed5c5mamjm

Optimizing high performance computing workflow for protein functional annotation

Larissa Stanberry, Bhanu Rekepalli, Yuan Liu, Paul Giblock, Roger Higdon, Elizabeth Montague, William Broomall, Natali Kolker, Eugene Kolker
2014 Concurrency and Computation  
The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins.  ...  Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding.  ...  BLAST and MUSCLE were designed to run on a typical workstation.  ... 
doi:10.1002/cpe.3264 pmid:25313296 pmcid:PMC4194055 fatcat:m4ygqcacgfcn3l2xeupme3qnuu

SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser

T. P. Walsh, C. Webber, S. Searle, S. S. Sturrock, G. J. Barton
2008 Nucleic Acids Research  
SCANPS performs iterative profile searching similar to PSI-BLAST but with full dynamic programing on each cycle and on-the-fly estimation of significance.  ...  This combination gives good sensitivity and selectivity that outperforms PSI-BLAST in domainsearching benchmarks.  ...  The MPI implementation gave parallel efficiency of over 90% on 16 processors on an Intel PIII cluster connected by 100 MB network.  ... 
doi:10.1093/nar/gkn320 pmid:18503088 pmcid:PMC2447745 fatcat:mk7dxo4nwvhbjjpj2wesdft7bm

SCBI_MapReduce, a New Ruby Task-Farm Skeleton for Automated Parallelisation and Distribution in Chunks of Sequences: The Implementation of a Boosted Blast+

Darío Guerrero-Fernández, Juan Falgueras, M. Gonzalo Claros
2013 Computational Biology Journal  
As proof-of-concept, distribution of a compiled version of BLAST+in the SCBI_DISTRIBUTED_BLASTgem is given, indicating that other blast binaries can be used while maintaining the same SCBI_DISTRIBUTED_BLASTcode  ...  It can be used from multicore workstations to heterogeneous grids. Tests have demonstrated that speed-up scales almost linearly and that distribution in small chunks increases it.  ...  Results indicate that SCBI MapReduce scales well, is fault-tolerant, can be used on multicore workstations, clusters, and heterogeneous grids, even where secured connections cannot be established, can  ... 
doi:10.1155/2013/707540 fatcat:uazcftq6pbhjvc2fuiosxbdame

On the Use of Social Networking Groups for Automatic Configuration of Virtual Grid Environments

Pierre St Juste, David Wolinsky, Jiangyan Xu, Michael Covington, Renato Figueiredo
2008 2008 Grid Computing Environments Workshop  
Social networking sites have enhanced the Web by providing online "communities" where users can easily create identities, establish relationships between identities, and share resources with one another  ...  To demonstrate the feasibility and usage of our approach, we developed a fully functional prototype implementation and present the quantitative results of our virtual private network.  ...  We believe that these issues will be addressed by social networking infrastructures as their API implementations mature. The granularity of Facebook access control is also another issue.  ... 
doi:10.1109/gce.2008.4738446 fatcat:kyuarfsn4bezzikvdffbbsxlje

FPGA-accelerated seed generation in Mercury BLASTP

Arpith Jacob, Joseph Lancaster, Jeremy Buhler, Roger D. Chamberlain
2007 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2007)  
In this paper, we focus on seed generation, the first stage of the BLASTP algorithm.  ...  In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more runtime or a cluster of machines to keep pace.  ...  The majority of high-performance BLAST solutions today are based on multiprocessor clusters [12, 16] .  ... 
doi:10.1109/fccm.2007.11 dblp:conf/fccm/JacobLBC07 fatcat:wchrhecpcnapvctw6y3fuh2acq
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