Current Issue : October - December Volume : 2011 Issue Number : 4 Articles : 5 Articles
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Background\r\nNext-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software.\r\nResults\r\nWe describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms.\r\nConclusion\r\nThe CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing....
The prevalence of multimedia applications has drastically increased the amount of multimedia data. With the drop of the hardware cost, more and more mobile devices with higher capacities are now used. The widely deployed wireless LAN and broadband wireless networks provide the ubiquitous network access for multimedia applications. Provision of Quality of Service (QoS) is challenging in mobile ad hoc networks because of the dynamic characteristics of mobile networks and the limited resources of the mobile devices. The wireless network is not reliable due to node mobility, multi-access channel and multi-hop communication. In this paper, we provide a survey of QoS provision in mobile multimedia, addressing the technologies at different network layers and cross-layer design. This paper focuses on the QoS techniques over IEEE 802.11e networks. We also provide some thoughts about the challenges and directions for future research....
Background\nThe widespread popularity of genomic applications is threatened by the ââ?¬Å?bioinformatics bottleneckââ?¬Â resulting from uncertainty about the cost and infrastructure needed to meet increasing demands for next-generation sequence analysis. Cloud computing services have been discussed as potential new bioinformatics support systems but have not been evaluated thoroughly.\nResults\nWe present benchmark costs and runtimes for common microbial genomics applications, including 16S rRNA analysis, microbial whole-genome shotgun (WGS) sequence assembly and annotation, WGS metagenomics and large-scale BLAST. Sequence dataset types and sizes were selected to correspond to outputs typically generated by small- to midsize facilities equipped with 454 and Illumina platforms, except for WGS metagenomics where sampling of Illumina data was used. Automated analysis pipelines, as implemented in the CloVR virtual machine, were used in order to guarantee transparency, reproducibility and portability across different operating systems, including the commercial Amazon Elastic Compute Cloud (EC2), which was used to attach real dollar costs to each analysis type. We found considerable differences in computational requirements, runtimes and costs associated with different microbial genomics applications. While all 16S analyses completed on a single-CPU desktop in under three hours, microbial genome and metagenome analyses utilized multi-CPU support of up to 120 CPUs on Amazon EC2, where each analysis completed in under 24 hours for less than $60. Representative datasets were used to estimate maximum data throughput on different cluster sizes and to compare costs between EC2 and comparable local grid servers.\nConclusions\nAlthough bioinformatics requirements for microbial genomics depend on dataset characteristics and the analysis protocols applied, our results suggests that smaller sequencing facilities (up to three Roche/454 or one Illumina GAIIx sequencer) invested in 16S rRNA amplicon sequencing, microbial single-genome and metagenomics WGS projects can achieve cost-efficient bioinformatics support using CloVR in combination with Amazon EC2 as an alternative to local computing centers....
Information systems are being shifted to scalable architectures like Cloud and peer-to-peer (P2P) models. In this paper, we consider the P2P model as a fully distributed, scalable system different from centralized coordinated systems in Cloud and Grid systems. A P2P system is composed of peer processes (peers). Here, applications are realized by activities of peers and cooperations among multiple peers. In P2P systems, since there is no centralized coordination, each peer has to obtain information about other peers by itself. In the group cooperation, each group member peer has to be trustworthy so that malicious behavior of a member peer cannot effect overall outcome of the whole group. Here, it is important to consider the trustworthiness of each group member as a base of an agreement procedure in the distributed environment. The goal of a group and the way to archive the goal are decided by the group members. During the agreement procedure, opinions of member peers have to be collected in a group. Malicious and unexpected behaviors of member peers can negatively effect the output of a group. Hence, it is significant to discuss how to compose a group only by including more trustworthy peers. In this paper, by taking advantage of the trustworthiness concept of each peer, we propose a novel approach to composing a trustworthy group in the distributed agreement protocols....
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