The Experts below are selected from a list of 42885 Experts worldwide ranked by ideXlab platform
Watts, Philip M - One of the best experts on this subject based on the ideXlab platform.
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A Low Latency Optical Switch for High Performance Computing with Minimized Processor Energy Load
Journal of Optical Communications and Networking, 2015Co-Authors: Liu Shiyun, Cheng Qixiang, Madarbux, Muhammad Ridwan, Wonfor Adrian, Penty Richard, White Ian, Watts, Philip MAbstract:Power density and cooling issues are limiting the performance of high performance chip multiprocessors (CMPs), and off-chip communications currently consume more than 20% of power for memory, coherence, PCI, and Ethernet links. Photonic transceivers integrated with CMPs are being developed to overcome these issues, potentially allowing low hop count switched connections between chips or data center Servers. However, latency in setting up optical connections is critically important in all computing applications, and having transceivers integrated on the processor chip also pushes other network functions and their associated power consumption onto the chip. In this paper, we propose a low latency optical switch architecture that minimizes the power consumed on the processor chip for two scenarios: multiple-socket shared memory coherence networks and optical top-of-rack switches for data centers. The switch architecture reduces power consumed on the CMP using a control plane with a simplified send and forget Server Interface and the use of a hybrid Mach–Zehnder interferometer and semiconductor optical amplifier integrated optical switch with electronic buffering. Results show that the proposed architecture offers a 42% reduction in head latency at low loads compared with a conventional scheduled optical switch as well as offering increased performance for streaming and incast traffic patterns. Power dissipated on the Server chip is shown to be reduced by more than 60% compared with a scheduled optical switch architecture with ring resonator switching.This work was supported by the UK Engineering and Physical Sciences Research Council (EPSRC) INTERNET program grant and an EPSRC Fellowship grant to Philip Watts. Both University College London and the University of Cambridge are members of GreenTouch.This paper was published in the Journal of Optical Communications and Networking and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: http://www.opticsinfobase.org/jocn/abstract.cfm?uri=jocn-7-3-A498. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law. This is the accepted manuscript of a paper published in the Journal of Optical Communications and Networking, Vol. 7, Issue 3, pp. A498-A510 (2015) http://dx.doi.org/10.1364/JOCN.7.00A49
Liu Shiyun - One of the best experts on this subject based on the ideXlab platform.
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A Low Latency Optical Switch for High Performance Computing with Minimized Processor Energy Load
Journal of Optical Communications and Networking, 2015Co-Authors: Liu Shiyun, Cheng Qixiang, Madarbux, Muhammad Ridwan, Wonfor Adrian, Penty Richard, White Ian, Watts, Philip MAbstract:Power density and cooling issues are limiting the performance of high performance chip multiprocessors (CMPs), and off-chip communications currently consume more than 20% of power for memory, coherence, PCI, and Ethernet links. Photonic transceivers integrated with CMPs are being developed to overcome these issues, potentially allowing low hop count switched connections between chips or data center Servers. However, latency in setting up optical connections is critically important in all computing applications, and having transceivers integrated on the processor chip also pushes other network functions and their associated power consumption onto the chip. In this paper, we propose a low latency optical switch architecture that minimizes the power consumed on the processor chip for two scenarios: multiple-socket shared memory coherence networks and optical top-of-rack switches for data centers. The switch architecture reduces power consumed on the CMP using a control plane with a simplified send and forget Server Interface and the use of a hybrid Mach–Zehnder interferometer and semiconductor optical amplifier integrated optical switch with electronic buffering. Results show that the proposed architecture offers a 42% reduction in head latency at low loads compared with a conventional scheduled optical switch as well as offering increased performance for streaming and incast traffic patterns. Power dissipated on the Server chip is shown to be reduced by more than 60% compared with a scheduled optical switch architecture with ring resonator switching.This work was supported by the UK Engineering and Physical Sciences Research Council (EPSRC) INTERNET program grant and an EPSRC Fellowship grant to Philip Watts. Both University College London and the University of Cambridge are members of GreenTouch.This paper was published in the Journal of Optical Communications and Networking and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: http://www.opticsinfobase.org/jocn/abstract.cfm?uri=jocn-7-3-A498. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law. This is the accepted manuscript of a paper published in the Journal of Optical Communications and Networking, Vol. 7, Issue 3, pp. A498-A510 (2015) http://dx.doi.org/10.1364/JOCN.7.00A49
Xiaowei Wang - One of the best experts on this subject based on the ideXlab platform.
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oncomir an online resource for exploring pan cancer microrna dysregulation
Bioinformatics, 2018Co-Authors: Nathan Wong, Yuhao Chen, Shuai Chen, Xiaowei WangAbstract:Summary Dysregulation of microRNAs (miRNAs) is extensively associated with cancer development and progression. miRNAs have been shown to be biomarkers for predicting tumor formation and outcome. However, identification of the relationships between miRNA expression and tumor characteristics can be difficult and time-consuming without appropriate bioinformatics expertise. To address this issue, we present OncomiR, an online resource for exploring miRNA dysregulation in cancer. Using combined miRNA-seq, RNA-seq and clinical data from The Cancer Genome Atlas, we systematically performed statistical analyses to identify dysregulated miRNAs that are associated with tumor development and progression in most major cancer types. Additional analyses further identified potential miRNA-gene target interactions in tumors. These results are stored in a backend database and presented through a web Server Interface. Moreover, through a backend bioinformatics pipeline, OncomiR can also perform dynamic analysis with custom miRNA selections for in-depth characterization of miRNAs in cancer. Availability and implementation The OncomiR website is freely accessible at www.oncomir.org. Contact xiaowei.wang@wustl.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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miRDB: An online resource for microRNA target prediction and functional annotations
Nucleic Acids Research, 2015Co-Authors: Nathan Wong, Xiaowei WangAbstract:MicroRNAs (miRNAs) are small non-coding RNAs that are extensively involved in many physiological and disease processes. One major challenge in miRNA studies is the identification of genes regulated by miRNAs. To this end, we have developed an online resource, miRDB (http://mirdb.org), for miRNA target prediction and functional annotations. Here, we describe recently updated features of miRDB, including 2.1 million predicted gene targets regulated by 6709 miRNAs. In addition to presenting precompiled prediction data, a new feature is the web Server Interface that allows submission of user-provided sequences for miRNA target prediction. In this way, users have the flexibility to study any custom miRNAs or target genes of interest. Another major update of miRDB is related to functional miRNA annotations. Although thousands of miRNAs have been identified, many of the reported miRNAs are not likely to play active functional roles or may even have been falsely identified as miRNAs from high-throughput studies. To address this issue, we have performed combined computational analyses and literature mining, and identified 568 and 452 functional miRNAs in humans and mice, respectively. These miRNAs, as well as associated functional annotations, are presented in the FuncMir Collection in miRDB.
Francine Blanchetsadri - One of the best experts on this subject based on the ideXlab platform.
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partial words and the critical factorization theorem revisited
Theoretical Computer Science, 2007Co-Authors: Francine Blanchetsadri, Nathan WetzlerAbstract:In this paper, we consider one of the most fundamental results on the periodicity of words, namely the critical factorization theorem. Given a word w and nonempty words u,v satisfying w=uv, the minimal local period associated with the factorization (u,v) is the length of the shortest square at position |u|-1. The critical factorization theorem shows that for any word, there is always a factorization whose minimal local period is equal to the minimal period (or global period) of the word. Crochemore and Perrin presented a linear time algorithm (in the length of the word) that finds a critical factorization from the computation of the maximal suffixes of the word with respect to two total orderings on words: the lexicographic ordering related to a fixed total ordering on the alphabet, and the lexicographic ordering obtained by reversing the order of letters in the alphabet. Here, by refining Crochemore and Perrin's algorithm, we give a version of the critical factorization theorem for partial words (such sequences may contain "do not know" symbols or "holes"). Our proof provides an efficient algorithm which computes a critical factorization when one exists. Our results extend those of Blanchet-Sadri and Duncan for partial words with one hole. A World Wide Web Server Interface at http://www.uncg.edu/mat/research/cft2/ has been established for automated use of the program.
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partial words and the critical factorization theorem
Journal of Combinatorial Theory Series A, 2005Co-Authors: Francine Blanchetsadri, S DuncanAbstract:The study of combinatorics on words, or finite sequences of symbols from a finite alphabet, finds applications in several areas of biology, computer science, mathematics, and physics. Molecular biology, in particular, has stimulated considerable interest in the study of combinatorics on partial words that are sequences that may have a number of "do not know" symbols also called "holes". This paper is devoted to a fundamental result on periods of words, the critical factorization theorem, which states that the period of a word is always locally detectable in at least one position of the word resulting in a corresponding critical factorization. Here, we describe precisely the class of partial words w with one hole for which the weak period is locally detectable in at least one position of w. Our proof provides an algorithm which computes a critical factorization when one exists. A World Wide Web Server Interface at http://www.uncg.edu/mat/cft/has been established for automated use of the program.
White Ian - One of the best experts on this subject based on the ideXlab platform.
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A Low Latency Optical Switch for High Performance Computing with Minimized Processor Energy Load
Journal of Optical Communications and Networking, 2015Co-Authors: Liu Shiyun, Cheng Qixiang, Madarbux, Muhammad Ridwan, Wonfor Adrian, Penty Richard, White Ian, Watts, Philip MAbstract:Power density and cooling issues are limiting the performance of high performance chip multiprocessors (CMPs), and off-chip communications currently consume more than 20% of power for memory, coherence, PCI, and Ethernet links. Photonic transceivers integrated with CMPs are being developed to overcome these issues, potentially allowing low hop count switched connections between chips or data center Servers. However, latency in setting up optical connections is critically important in all computing applications, and having transceivers integrated on the processor chip also pushes other network functions and their associated power consumption onto the chip. In this paper, we propose a low latency optical switch architecture that minimizes the power consumed on the processor chip for two scenarios: multiple-socket shared memory coherence networks and optical top-of-rack switches for data centers. The switch architecture reduces power consumed on the CMP using a control plane with a simplified send and forget Server Interface and the use of a hybrid Mach–Zehnder interferometer and semiconductor optical amplifier integrated optical switch with electronic buffering. Results show that the proposed architecture offers a 42% reduction in head latency at low loads compared with a conventional scheduled optical switch as well as offering increased performance for streaming and incast traffic patterns. Power dissipated on the Server chip is shown to be reduced by more than 60% compared with a scheduled optical switch architecture with ring resonator switching.This work was supported by the UK Engineering and Physical Sciences Research Council (EPSRC) INTERNET program grant and an EPSRC Fellowship grant to Philip Watts. Both University College London and the University of Cambridge are members of GreenTouch.This paper was published in the Journal of Optical Communications and Networking and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: http://www.opticsinfobase.org/jocn/abstract.cfm?uri=jocn-7-3-A498. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law. This is the accepted manuscript of a paper published in the Journal of Optical Communications and Networking, Vol. 7, Issue 3, pp. A498-A510 (2015) http://dx.doi.org/10.1364/JOCN.7.00A49
