Necessity is the mother of invention: a simple grid computing system using commodity tools

Myers, Daniel S.; Cummings, Michael P.

doi:10.1016/s0743-7315(03)00004-2

Cited by 37 publications

(20 citation statements)

References 12 publications

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“…Grid computing through the Lattice Project (47) was used to decrease the computational time required to complete the best tree search and the bootstrap replicates for the data set. The GARLI executable was converted to a grid service such that batches of bootstrap replicates were distributed among hundreds of computers, where they were conducted asynchronously and in parallel (48,49).…”

Section: Methodsmentioning

confidence: 99%

Genetic Diversity and Evolution of Salmonella enterica Serovar Enteritidis Strains with Different Phage Types

et al. 2014

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c Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar Enteritidis for over 2 decades. However, knowledge of the genetic and evolutionary relationships between phage types is very limited, making differences difficult to interpret. Here, single nucleotide polymorphisms (SNPs) identified from whole-genome comparisons were used to determine the relationships between some S. Enteritidis phage types (PTs) commonly associated with food-borne outbreaks in the United States. Emphasis was placed on the predominant phage types PT8, PT13a, and PT13 in North America. With >89,400 bp surveyed across 98 S. Enteritidis isolates representing 14 distinct phage types, 55 informative SNPs were discovered within 23 chromosomally anchored loci. To maximize the discriminatory and evolutionary partitioning of these highly homogeneous strains, sequences comprising informative SNPs were concatenated into a single combined data matrix and subjected to phylogenetic analysis. The resultant phylogeny allocated most S. Enteritidis isolates into two distinct clades (clades I and II) and four subclades. Synapomorphic (shared and derived) sets of SNPs capable of distinguishing individual clades/subclades were identified. However, individual phage types appeared to be evolutionarily disjunct when mapped to this phylogeny, suggesting that phage typing may not be valid for making phylogenetic inferences. Furthermore, the set of SNPs identified here represents useful genetic markers for strain differentiation of more clonal S. Enteritidis strains and provides core genotypic markers for future development of a SNP typing scheme with S. Enteritidis.

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Section: Methodsmentioning

confidence: 99%

Genetic Diversity and Evolution of Salmonella enterica Serovar Enteritidis Strains with Different Phage Types

et al. 2014

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“…Parallel computation has been successfully used in previous large-scale computer-based studies in phylogenetics (Cummings et al, 1995(Cummings et al, , 1999Otto et al, 1996). We developed our own Grid computing system using standard software components (Myers and Cummings, 2003) to distribute the independent analyses across multiple computer systems and geographic locations. The principal part of the simulations took 15.68 CPU years (wallclock) to complete, the comparison of bootstrap procedures required an additional 88.08 CPU days, and the star topology analyses required 5.35 CPU days.…”

Section: Computationmentioning

confidence: 99%

Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case

Cummings¹,

Handley²,

Myers³

et al. 2003

Systematic Biology

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280

102

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Assessment of the reliability of a given phylogenetic hypothesis is an important step in phylogenetic analysis. Historically, the nonparametric bootstrap procedure has been the most frequently used method for assessing the support for specific phylogenetic relationships. The recent employment of Bayesian methods for phylogenetic inference problems has resulted in clade support being expressed in terms of posterior probabilities. We used simulated data and the four-taxon case to explore the relationship between nonparametric bootstrap values (as inferred by maximum likelihood) and posterior probabilities (as inferred by Bayesian analysis). The results suggest a complex association between the two measures. Three general regions of tree space can be identified: (1) the neutral zone, where differences between mean bootstrap and mean posterior probability values are not significant, (2) near the two-branch corner, and (3) deep in the two-branch corner. In the last two regions, significant differences occur between mean bootstrap and mean posterior probability values. Whether bootstrap or posterior probability values are higher depends on the data in support of alternative topologies. Examination of star topologies revealed that both bootstrap and posterior probability values differ significantly from theoretical expectations; in particular, there are more posterior probability values in the range 0.85-1 than expected by theory. Therefore, our results corroborate the findings of others that posterior probability values are excessively high. Our results also suggest that extrapolations from single topology branch-length studies are unlikely to provide any general conclusions regarding the relationship between bootstrap and posterior probability values.

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“…This research program focuses on problems in molecular evolution and genetics, which often require approaches that are very computation-intensive. Our need for computer resources for our work led to the development of a simple Grid computing system using commodity tools [23], which was used for a large-scale simulation study [9]. Our subsequent work has made use of the Grid middleware Globus [12] and the Berkeley Open Infrastructure for Network Computing (BOINC) [3,7], and focused on expanding the reach of Grid computing by creating a system that combines these two models (Myers, Bazinet and Cummings, in preparation).…”

Section: Introductionmentioning

confidence: 99%

Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services

Bazinet

Myers

Fuetsch

et al. 2007

Future Generation Computer Systems

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Necessity is the mother of invention: a simple grid computing system using commodity tools

Cited by 37 publications

References 12 publications

Genetic Diversity and Evolution of Salmonella enterica Serovar Enteritidis Strains with Different Phage Types

Genetic Diversity and Evolution of Salmonella enterica Serovar Enteritidis Strains with Different Phage Types

Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case

Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services

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