The Ultralight project: the network as an integrated and managed resource for data-intensive science

Looks at the UltraLight project which treats the network interconnecting globally distributed data sets as a dynamic, configurable, and closely monitored resource to construct a next-generation system that can meet the high-energy physics community's data-processing, distribution, access, and analysis needs

The Design and Demonstration of the Ultralight Testbed

In this paper we present the motivation, the design, and a recent demonstration of the UltraLight testbed at SC|05. The goal of the Ultralight testbed is to help meet the data-intensive computing challenges of the next generation of particle physics experiments with a comprehensive, network- focused approach. UltraLight adopts a new approach to networking: instead of treating it traditionally, as a static, unchanging and unmanaged set of inter-computer links, we are developing and using it as a dynamic, configurable, and closely monitored resource that is managed from end-to-end. To achieve its goal we are constructing a next-generation global system that is able to meet the data processing, distribution, access and analysis needs of the particle physics community. In this paper we will first present early results in the various working areas of the project. We then describe our experiences of the network architecture, kernel setup, application tuning and configuration used during the bandwidth challenge event at SC|05. During this Challenge, we achieved a record-breaking aggregate data rate in excess of 150 Gbps while moving physics datasets between many Grid computing sites

The Motivation, Architecture and Demonstration of Ultralight Network Testbed

In this paper we describe progress in the NSF-funded Ultralight project and a recent demonstration of Ultralight technologies at SuperComputing 2005 (SC|05). The goal of the Ultralight project is to help meet the data-intensive computing challenges of the next generation of particle physics experiments with a comprehensive, network-focused approach. Ultralight adopts a new approach to networking: instead of treating it traditionally, as a static, unchanging and unmanaged set of inter-computer links, we are developing and using it as a dynamic, configurable, and closely monitored resource that is managed from end-to-end. Thus we are constructing a next-generation global system that is able to meet the data processing, distribution, access and analysis needs of the particle physics community. In this paper we present the motivation for, and an overview of, the Ultralight project. We then cover early results in the various working areas of the project. The remainder of the paper describes our experiences of the Ultralight network architecture, kernel setup, application tuning and configuration used during the bandwidth challenge event at SC|05. During this Challenge, we achieved a record-breaking aggregate data rate in excess of 150 Gbps while moving physics datasets between many sites interconnected by the Ultralight backbone network. The exercise highlighted the benefits of Ultralight's research and development efforts that are enabling new and advanced methods of distributed scientific data analysis

The Design and Implementation of the Transatlantic Mission-Oriented Production and Experimental Networks

In this paper we present the design and implementation of the mission-oriented USLHCNet for HEP research community and the UltraLight network testbed. The design philosophy for these networks is to help meet the data-intensive computing challenges of the next generation of particle physics experiments with a comprehensive, network-focused approach. Instead of treating the network as a static, unchanging and unmanaged set of intercomputer links, we are developing and using it as a dynamic, configurable, and closely monitored resource that is managed from end-to-end. In this paper we will present our work in the various areas of the project including infrastructure construction, protocol research and application development. Our goal is to construct a next-generation global system that is able to meet the data processing, distribution, access and analysis needs of the particle physics community

Sequencing and characterization of Varicella-Zoster virus vaccine strain SuduVax

<p>Abstract</p> <p>Background</p> <p>Varicella-zoster virus (VZV) causes chickenpox in children and shingles in older people. Currently, live attenuated vaccines based on the Oka strain are available worldwide. In Korea, an attenuated VZV vaccine has been developed from a Korean isolate and has been commercially available since 1994. Despite this long history of use, the mechanism for the attenuation of the vaccine strain is still elusive. We attempted to understand the molecular basis of attenuation mechanism by full genome sequencing and comparative genomic analyses of the Korean vaccine strain SuduVax.</p> <p>Results</p> <p>SuduVax was found to contain a genome that was 124,759 bp and possessed 74 open reading frames (ORFs). SuduVax was genetically most close to Oka strains and these Korean-Japanese strains formed a strong clade in phylogenetic trees. SuduVax, similar to the Oka vaccine strains, underwent T- > C substitution at the stop codon of ORF0, resulting in a read-through mutation to code for an extended form of ORF0 protein. SuduVax also shared certain deletion and insertion mutations in ORFs 17, 29, 56 and 60 with Oka vaccine strains and some clinical strains.</p> <p>Conclusions</p> <p>The Korean VZV vaccine strain SuduVax is genetically similar to the Oka vaccine strains. Further comparative genomic and bioinformatics analyses will help to elucidate the molecular basis of the attenuation of the VZV vaccine strains.</p

Risk of Cancer in Patients with Insomnia, Parasomnia, and Obstructive Sleep Apnea: A Nationwide Nested Case-Control Study

Abstract Purpose: Insomnia, parasomnia, and obstructive sleep apnea have been associated with a number of disease pathologies, but little is known about the relationship of these sleep disorders and cancer. The study explored the risk of sleep disorder (SD)-induced cancer using nationwide population data. Two million data from the National Health Insurance system of Taiwan was used to assess for the relationship. Patients and Methods: Patients with cancer as our cases and patients without cancer as our control group in 2001-20011. The study patients were traced back to seek the exposure risk factor of sleep disorders, which was divided into three categories: insomnia, obstructive sleep apnea (OSA) and parasomnia. Patients were selected excluding patients who had cancer prior to presenting with the sleep disorder and the person-year is less than 2 years. Each case was randomly matched with two cases with the same age, gender, and index year. Results: There were significantly increased risks of breast cancer in the patients with insomnia (AHR=1.73; 95% CI: 1.57−1.90), patients with parasomnia (AHR=2.76; 95% CI: 1.53−5.00), and patients with OSA (AHR=2.10; 95% CI: 1.16−3.80). Moreover, patients with parasomnia had significantly higher risk of developing oral cancer (AHR=2.71; 95% CI: 1.02−7.24) compared with patients without parasomnia. The risk of suffering from nasal cancer (AHR=5.96, 95% CI: 2.96−11.99) and prostate cancer (AHR=3.69, 95% CI: 1.98− 6.89) in patients with OSA was significantly higher than that of patients without OSA. Conclusions: Our findings provided the evidence that people diagnosed with insomnia, parasomnia and OSA are at a higher risk of developing cancers to remind people to improve sleep quality

The Ultralight project: The Network as an Integrated and Managed Resource for Data Intensive Science

We describe the NSF-funded UltraLight project. The project’s goal is to meet the data-intensive computing challenges of the next generation of particle physics experiments with a comprehensive, network-focused agenda. In particular we argue that instead of treating the network traditionally, as a static, unchanging and unmanaged set of inter-computer links, we instead will use it as a dynamic, configurable, and closely monitored resource, managed end-toend, to construct a next-generation global system able to meet the data processing, distribution, access and analysis needs of the high energy physics (HEP) community. While the initial UltraLight implementation and services architecture is being developed to serve HEP, we expect many of UltraLight’s developments in the areas of networking, monitoring, management, and collaborative research, to be applicable to many fields of data intensive e-science. In this paper we give an overview of, and motivation for the UltraLight project, and provide early results within different working areas of the project

The Motivation, Architecture and Demonstration of Ultralight Network Testbed

In this paper we describe progress in the NSF-funded Ultralight project and a recent demonstration of Ultralight technologies at SuperComputing 2005 (SC|05). The goal of the Ultralight project is to help meet the data-intensive computing challenges of the next generation of particle physics experiments with a comprehensive, network-focused approach. Ultralight adopts a new approach to networking: instead of treating it traditionally, as a static, unchanging and unmanaged set of inter-computer links, we are developing and using it as a dynamic, configurable, and closely monitored resource that is managed from end-to-end. Thus we are constructing a next-generation global system that is able to meet the data processing, distribution, access and analysis needs of the particle physics community. In this paper we present the motivation for, and an overview of, the Ultralight project. We then cover early results in the various working areas of the project. The remainder of the paper describes our experiences of the Ultralight network architecture, kernel setup, application tuning and configuration used during the bandwidth challenge event at SC|05. During this Challenge, we achieved a record-breaking aggregate data rate in excess of 150 Gbps while moving physics datasets between many sites interconnected by the Ultralight backbone network. The exercise highlighted the benefits of Ultralight&apos;s research and development efforts that are enabling new and advanced methods of distributed scientific data analysis