BioSPLASH: A Sample Workload For Bioinformatics And Computational Biology For Optimizing Next - Gen

A disposable pad for use with a surgical instrument having a supporting element. The pad includes a flexible elongated member having a channel therein for slidably receiving the supporting element. A stop member limits longitudinal insertion of the supporting element into the channel, a retention member prevents lateral movement of the supporting element out of the channel, and a latching member secures the supporting element against longitudinal displacement from the channel. The latching member is normally disposed in a latching position but is shiftable into a releasing position as the elongated member is flexed to remove the pad. The supporting element of the surgical instrument can hold an artery or vein or other body tissue without damage when using the disposable pad.

[1]  David A. Bader,et al.  Incorporating life sciences applications in the architectural optimizations of next-generation petaflop-system , 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).

[2]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[3]  David A. Bader.  Computational biology and high-performance computing , 2004, CACM.

[4]  Brad Calder,et al.  Automatically characterizing large scale program behavior , 2002, ASPLOS X.

[5]  David A. Bader,et al.  A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study , 2001, WADS.

[6]  P E Bourne,et al.  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.

[7]  M. P. Cummings.  PHYLIP (Phylogeny Inference Package) , 2004 .

[8]  Kuo-Bin Li,et al.  ClustalW-MPI: ClustalW analysis using distributed and parallel computing , 2003, Bioinform..

[9]  Eric Stahlberg,et al.  Improving performance of multiple sequence alignment analysis in multi-client environments , 2002, Proceedings 16th International Parallel and Distributed Processing Symposium.

[10]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[11]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[12]  J. Weber,et al.  Human whole-genome shotgun sequencing. , 1997, Genome research.

[13]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[14]  biyofizik Biyokimya,et al.  The European Molecular Biology Laboratory , 2011, Current Biology.

[15]  Anoop Gupta,et al.  The SPLASH-2 programs: characterization and methodological considerations , 1995, ISCA.

[16]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[17]  James L. Peterson,et al.  Design and validation of a performance and power simulator for PowerPC systems , 2003, IBM J. Res. Dev..

[18]  S. Salzberg,et al.  Microbial gene identification using interpolated Markov models. , 1998, Nucleic acids research.

[19]  Anoop Gupta,et al.  SPLASH: Stanford parallel applications for shared-memory , 1992, CARN.

[20]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[21]  Lixin Zhang,et al.  Mambo: a full system simulator for the PowerPC architecture , 2004, PERV.

[22]  Breakpoint Phylogenies. , 1997, Genome informatics. Workshop on Genome Informatics.

[23]  Amitava Datta,et al.  Multiple sequence alignment in parallel on a workstation cluster , 2004, Bioinform..

[24]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[25]  David A. Bader,et al.  BioPerf: a benchmark suite to evaluate high-performance computer architecture on bioinformatics applications , 2005, IEEE International. 2005 Proceedings of the IEEE Workload Characterization Symposium, 2005..

[26]  Eugene W. Myers,et al.  Algorithms for whole genome shotgun sequencing , 1999, RECOMB.

[27]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[28]  S. Salzberg,et al.  Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.

[29]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[30]  Donald Yeung,et al.  BioBench: A Benchmark Suite of Bioinformatics Applications , 2005, IEEE International Symposium on Performance Analysis of Systems and Software, 2005. ISPASS 2005..

[31]  Anoop Gupta,et al.  Complete computer system simulation: the SimOS approach , 1995, IEEE Parallel Distributed Technol. Syst. Appl..

[32]  Olivier Poch,et al.  A comprehensive comparison of multiple sequence alignment programs , 1999, Nucleic Acids Res..

[33]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.