scholarly journals Experiences with Resource Provisioning for Scientific Workflows Using Corral

2010 ◽  
Vol 18 (2) ◽  
pp. 77-92 ◽  
Author(s):  
Gideon Juve ◽  
Ewa Deelman ◽  
Karan Vahi ◽  
Gaurang Mehta
Keyword(s):  
Large Scale ◽  
Genome Mapping ◽  
Resource Provisioning ◽  
Distributed Resources ◽  
Local Cluster ◽  
Loosely Coupled ◽  
Large Numbers ◽  
A Genome ◽  
Order Of Magnitude ◽  
Level Scheduling

The development of grid and workflow technologies has enabled complex, loosely coupled scientific applications to be executed on distributed resources. Many of these applications consist of large numbers of short-duration tasks whose runtimes are heavily influenced by delays in the execution environment. Such applications often perform poorly on the grid because of the large scheduling overheads commonly found in grids. In this paper we present a provisioning system based on multi-level scheduling that improves workflow runtime by reducing scheduling overheads. The system reserves resources for the exclusive use of the application, and gives applications control over scheduling policies. We describe our experiences with the system when running a suite of real workflow-based applications including in astronomy, earthquake science, and genomics. Provisioning resources with Corral ahead of the workflow execution, reduced the runtime of the astronomy application by up to 78% (45% on average) and of a genome mapping application by an order of magnitude when compared to traditional methods. We also show how provisioning can benefit applications both on a small local cluster as well as a large-scale campus resource.

Large-scale mutagenesis directed at specific chromosomes in wheat

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 45-49 ◽  
Author(s):  
Robert Koebner ◽  
James Hadfield
Keyword(s):  
Disease Resistance ◽  
Large Scale ◽  
Target Gene ◽  
Yellow Rust ◽  
Chemical Mutagenesis ◽  
Loss Of Function ◽  
Novel Approach ◽  
Large Numbers ◽  
Resistance Pathway ◽  
Order Of Magnitude

A novel approach has been developed to allow for the efficient selection of loss-of-function wheat mutants in the M1 generation, following either physical or chemical mutagenesis. This has generated an order of magnitude increase in the efficiency of identification of mutants, and also greatly increases the likelihood that selected individuals reflect mutation events at the target locus, rather than at genes acting elsewhere in the disease resistance pathway. The approach relies only on prior knowledge of the chromosomal location of the target gene, and uses the polyploidy of wheat to construct populations for mutagenesis in which large numbers of individuals are hemizygous for the target gene. The idea is illustrated with the mass identification of mutants at three independent genes for race-specific resistance to yellow rust, and one gene for resistance to powdery mildew.Key words: disease resistance mutant, hemizygotes, loss-of-function mutant.

scholarly journals Clusters in the Optical

2005 ◽  
Vol 13 ◽  
pp. 286-290
Author(s):  
Lori M. Lubin
Keyword(s):  
Large Scale ◽  
Clusters Of Galaxies ◽  
Large Area ◽  
Cluster Galaxy ◽  
Local Cluster ◽  
Detection Techniques ◽  
Large Numbers ◽  
Global Cluster ◽  
Cluster Properties ◽  
Galaxy Populations

AbstractI present a brief review of studies of galaxy clusters in the optical. Clusters of galaxies were historically detected in the optical, and this selection provided the first large, statistical samples of clusters. I describe how these samples have been instrumental in characterizing the properties of the local cluster population, tracing large scale structure, and constraining cosmology. More sophisticated cluster detection techniques in the optical have now made it possible to detect large numbers of clusters up to z ~ 1.4. I describe these advances and discuss how large-area and deep surveys are being used to determine the evolution in the global cluster properties and the properties of cluster galaxy populations.

scholarly journals Efficient large-scale replica-exchange simulations on production infrastructure

2011 ◽  
Vol 369 (1949) ◽  
pp. 3318-3335 ◽  
Author(s):  
Abhinav Thota ◽  
André Luckow ◽  
Shantenu Jha
Keyword(s):  
Large Scale ◽  
Coordination Mechanisms ◽  
Replica Exchange ◽  
Distributed Resources ◽  
Loosely Coupled ◽  
Asynchronous Algorithms ◽  
Folding Dynamics ◽  
Binding Affinity Calculations ◽  
Physical Phenomena ◽  
Distributed Infrastructure

Replica-exchange (RE) algorithms are used to understand physical phenomena—ranging from protein folding dynamics to binding affinity calculations. They represent a class of algorithms that involve a large number of loosely coupled ensembles, and are thus amenable to using distributed resources. We develop a framework for RE that supports different replica pairing (synchronous versus asynchronous) and exchange coordination mechanisms (centralized versus decentralized) and which can use a range of production cyberinfrastructures concurrently. We characterize the performance of both RE algorithms at an unprecedented number of cores employed—the number of replicas and the typical number of cores per replica—on the production distributed infrastructure. We find that the asynchronous algorithms outperform the synchronous algorithms, even though details of the specific implementations are important determinants of performance.

Computer Analyses in Preventive Health Research

1967 ◽  
Vol 06 (01) ◽  
pp. 8-14 ◽  
Author(s):  
M. F. Collen
Keyword(s):  
Medical Research ◽  
Preventive Medicine ◽  
Health Research ◽  
Large Scale ◽  
Preventive Health ◽  
New Era ◽  
Large Numbers ◽  
Normal Test ◽  
Computer Analyses

The utilization of an automated multitest laboratory as a data acquisition center and of a computer for trie data processing and analysis permits large scale preventive medical research previously not feasible. Normal test values are easily generated for the particular population studied. Long-term epidemiological research on large numbers of persons becomes practical. It is our belief that the advent of automation and computers has introduced a new era of preventive medicine.

scholarly journals Nebula: ultra-efficient mapping-free structural variant genotyper

2021 ◽  
Author(s):  
Parsoa Khorsand ◽  
Fereydoun Hormozdiari
Keyword(s):  
Large Scale ◽  
Structural Variants ◽  
Sequencing Technologies ◽  
Generic Framework ◽  
Common Genetic Variants ◽  
Order Of Magnitude ◽  
Complex Events ◽  
Comparable Accuracy ◽  
Using Data ◽  
Computational Resources

Abstract Large scale catalogs of common genetic variants (including indels and structural variants) are being created using data from second and third generation whole-genome sequencing technologies. However, the genotyping of these variants in newly sequenced samples is a nontrivial task that requires extensive computational resources. Furthermore, current approaches are mostly limited to only specific types of variants and are generally prone to various errors and ambiguities when genotyping complex events. We are proposing an ultra-efficient approach for genotyping any type of structural variation that is not limited by the shortcomings and complexities of current mapping-based approaches. Our method Nebula utilizes the changes in the count of k-mers to predict the genotype of structural variants. We have shown that not only Nebula is an order of magnitude faster than mapping based approaches for genotyping structural variants, but also has comparable accuracy to state-of-the-art approaches. Furthermore, Nebula is a generic framework not limited to any specific type of event. Nebula is publicly available at https://github.com/Parsoa/Nebula.

scholarly journals Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1765-1778
Author(s):  
Gregory J Budziszewski ◽  
Sharon Potter Lewis ◽  
Lyn Wegrich Glover ◽  
Jennifer Reineke ◽  
Gary Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Translocation ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Lethal Mutant ◽  
A Genome ◽  
Genes Encoding ◽  
High Level ◽  
Mutant Lines ◽  
Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

scholarly journals A Survey on Edge Performance Benchmarking

2021 ◽  
Vol 54 (3) ◽  
pp. 1-33
Author(s):  
Blesson Varghese ◽  
Nan Wang ◽  
David Bermbach ◽  
Cheol-Ho Hong ◽  
Eyal De Lara ◽  
...  
Keyword(s):  
Large Scale ◽  
Future Internet ◽  
Coupled Systems ◽  
Operational Conditions ◽  
Loosely Coupled ◽  
Performance Benchmarking ◽  
The Past ◽  
Geographically Dispersed ◽  
Tightly Coupled ◽  
History Of

Edge computing is the next Internet frontier that will leverage computing resources located near users, sensors, and data stores to provide more responsive services. Therefore, it is envisioned that a large-scale, geographically dispersed, and resource-rich distributed system will emerge and play a key role in the future Internet. However, given the loosely coupled nature of such complex systems, their operational conditions are expected to change significantly over time. In this context, the performance characteristics of such systems will need to be captured rapidly, which is referred to as performance benchmarking, for application deployment, resource orchestration, and adaptive decision-making. Edge performance benchmarking is a nascent research avenue that has started gaining momentum over the past five years. This article first reviews articles published over the past three decades to trace the history of performance benchmarking from tightly coupled to loosely coupled systems. It then systematically classifies previous research to identify the system under test, techniques analyzed, and benchmark runtime in edge performance benchmarking.

scholarly journals Relaxation Times in Strictly Disk Systems

1971 ◽  
Vol 10 ◽  
pp. 15-19
Author(s):  
George B. Rybicki
Keyword(s):  
Numerical Experiments ◽  
Relaxation Times ◽  
Galactic Structure ◽  
Large Numbers ◽  
Order Of Magnitude ◽  
Vlasov Limit ◽  
The Mean ◽  
Gravitating Systems

AbstractIt is shown that the time of relaxation by particle encounters of self-gravitating systems in the plane interacting by 1/r2 forces is of the same order of magnitude as the mean orbit time. Therefore such a system does not have a Vlasov limit for large numbers of particles, unless appeal is made to some non-zero thickness of the disk. The relevance of this result to numerical experiments on galactic structure is discussed.

scholarly journals Genetic variation in recombination rate in the pig

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Material ◽  
A Genome ◽  
Pig Genome ◽  
Genetic Length ◽  
Trait Locus ◽  
Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

scholarly journals Development of a Radar Reflector Kit for Older Adults to Use to Signal Their Location and Needs in a Large-Scale Earthquake Disaster

2021 ◽  
Vol 13 (10) ◽  
pp. 1883
Author(s):  
Yuma Morisaki ◽  
Makoto Fujiu ◽  
Ryoichi Furuta ◽  
Junichi Takayama
Keyword(s):  
Older Adults ◽  
Synthetic Aperture Radar ◽  
Satellite Imagery ◽  
Disaster Response ◽  
Large Scale ◽  
Synthetic Aperture ◽  
Earthquake Disaster ◽  
Large Numbers ◽  
The World ◽  
Vulnerable People

In Japan, older adults account for the highest proportion of the population of any country in the world. When large-scale earthquake disasters strike, large numbers of casualties are known to particularly occur among seniors. Many are physically or mentally vulnerable and require assistance during the different phases of disaster response, including rescue, evacuation, and living in an evacuation center. However, the growing number of older adults has made it difficult, after a disaster, to quickly gather information on their locations and assess their needs. The authors are developing a proposal to enable vulnerable people to signal their location and needs in the aftermath of a disaster to response teams by deploying radar reflectors that can be detected in synthetic aperture radar (SAR) satellite imagery. The purpose of this study was to develop a radar reflector kit that seniors could easily assemble in order to make this proposal feasible in practice. Three versions of the reflector were tested for detectability, and a sample of older adults was asked to assemble the kits and provide feedback regarding problems they encountered and regarding their interest in using the reflectors in the event of a large-scale disaster.

Sign in / Sign up

Export Citation Format

Share Document