38,584 research outputs found

    Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

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    BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum

    Resilient random modulo cache memories for probabilistically-analyzable real-time systems

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    Fault tolerance has often been assessed separately in safety-related real-time systems, which may lead to inefficient solutions. Recently, Measurement-Based Probabilistic Timing Analysis (MBPTA) has been proposed to estimate Worst-Case Execution Time (WCET) on high performance hardware. The intrinsic probabilistic nature of MBPTA-commpliant hardware matches perfectly with the random nature of hardware faults. Joint WCET analysis and reliability assessment has been done so far for some MBPTA-compliant designs, but not for the most promising cache design: random modulo. In this paper we perform, for the first time, an assessment of the aging-robustness of random modulo and propose new implementations preserving the key properties of random modulo, a.k.a. low critical path impact, low miss rates and MBPTA compliance, while enhancing reliability in front of aging by achieving a better – yet random – activity distribution across cache sets.Peer ReviewedPostprint (author's final draft
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