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16th international Euro-Par conference on Parallel Processing, Euro-Par 2010

ISBN: (纸本)9783642152764

the proceedings contain 104 papers. the special focus in this conference is on Parallel Processing. the topics include: A parallel implementation of the Jacobi-Davidson eigensolver and its application in a plasma turbulence code;scheduling parallel eigenvalue computations in a quantum chemistry code;Scalable parallelization strategies to accelerate NuFFT data translation on multicores;multicore and Manycore programming;javaSymphony: A programming and execution environment for parallel and distributed many-core architectures;scalable producer-consumer pools based on elimination-diffraction trees;productivity and performance: Improving consumability of hardware transactional memory through a real-world case study;exploiting fine-grained parallelism on cell processors;optimized on-chip-pipelined mergesort on the cell/B.E.;transactional mutex locks;Near-optimal placement of MPI processes on hierarchical NUMA architectures;parallel enumeration of shortest lattice vectors;A parallel GPU algorithm for mutual information based 3D nonrigid image registration;Multi-GPU and multi-CPU parallelization for interactive physics simulations;Long dna sequence comparison on multicore architectures;adaptive fault tolerance for many-core based space-borne computing;Maestro: Data orchestration and tuning for openCL devices;multithreaded Geant4: Semi-automatic transformation into scalable thread-parallel software;parallel exact time series motif discovery;optimized dense matrix multiplication on a many-core architecture;exceptions for algorithmic skeletons;a language-based tuning mechanism for task and pipeline parallelism;A study of a software cache implementation of the OpenMP memory model for multicore and manycore architectures;programming CUDA-based GPuS to simulate two-layer shallow water flows;theory and algorithms for parallel computation;analysis of multi-organization scheduling algorithms;Area-maximizing schedules for series-parallel DAGs;parallel Selection by Regular Sampling;a

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16th international Euro-Par conference on Parallel Processing, Euro-Par 2010

16th International Euro-Par Conference on Parallel Processin...

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16th international Euro-Par conference on Parallel Processing, Euro-Par 2010

ISBN: (纸本)9783642152900

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Long dna Sequence Comparison on Multicore Architectures

Long DNA Sequence Comparison on Multicore Architectures

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16th international Euro-Par conference on Parallel Processing

作者： Sanchez, Friman Cabarcas, Felipe Ramirez, Alex Valero, Mateo Tech Univ Catalonia Barcelona Spain Barcelona Supercomp Ctr Barcelona Spain Univ Antioquia Antioquia Colombia

ISBN: (纸本)9783642152900

Biological sequence comparison is one of the most important tasks in Bioinformatics. Due to the growth of biological databases, sequence comparison is becoming an important challenge for high performance computing, especially when very long sequences are compared. the Smith-Waterman (SW) algorithm is an exact method based on dynamic programming to quantify local similarity between sequences. the inherent large parallelism of the algorithm makes it ideal for architectures supporting multiple dimensions of parallelism (TLP, DLP and ILP). In this work, we show how long sequences comparison takes advantage of current and future multicore architectures. We analyze two different SW implementations on the CellBE and use simulation tools to study the performance scalability in a multicore architecture. We study the memory organization that delivers the maximum bandwidth with the minimum cost. Our results show that a heterogeneous architecture is an valid alternative to execute challenging bioinformatic workloads.

关键词： Bioinformatics

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dna computing and molecular programming - 15th international conference, dna 15, Revised Selected Papers

DNA Computing and Molecular Programming - 15th International...

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15th international conference on dna computing and molecular programming, dna 15

ISBN: (纸本)364210603X

the proceedings contain 16 papers. the topics discussed include: filter position in networks of evolutionary processors does not matter: a direct proof;strand algebras for dna computing;a domain-specific language for programming in the tile assembly model;advancing the deoxyribozyme-based logic gate design process;dna chips for species identification and biological phylogenies;renewable, time-responsive dna logic gates for scalable digital circuits;self-assembly of the discrete Sierpinski carpet and related fractals;automatic design of dna logic gates based on kinetic simulation;design of a biomolecular device that executes process algebra;the effect of malformed tiles on tile assemblies within kTAM;positional state representation and its transition control for photonic dna automation;construction of AND gate for RTRACS with the capacity of extension to NAND gate;and time-complexity of multilayered dna strand displacement circuits.

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dna Chips for Species Identification and Biological Phylogenies

DNA Chips for Species Identification and Biological Phylogen...

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15th international conference on dna computing and molecular programming

作者： Garzon, Max H. Wong, Tit-Yee Phan, Vinhthuy Univ Memphis Memphis TN 38152 USA

ISBN: (纸本)9783642106033

the codeword design problem is an important problem in dna computing and its applications. Several theoretical analyses as well as practical solutions for short oligonucleotides (up to 20-mers) have been generated recently. these solutions have, in turn, suggested new applications to dna-based indexing and natural language processing, in addition to the obvious applications to the problems of reliability and scalability that generated them. Here we continue the exploration of this type of dna-based indexing for biological applications and show that dna noncrosshybridizing (nxh) sets can be successfully applied to infer ab initio phylogenetic trees by providing a way to measure distances among different genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. these phylogenies are solidly established and well accepted in biology. the new technique is much more effective in terms of signal-to-noise ratio, cost and time than current methods. Second, it can be scaled up to newly available universal dna chips readily available both in vitro and in silica. In particular, we show how a recently obtained such set of nxh 16-mers can be used as a universal coordinate system in dna spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform reference system, a veritable and comprehensive "Atlas of Life", as it is or as it could be on earth.

关键词： dna codeword design noncrosshybridizing oligonucleotide bases phylogenetic analysis genomic signatures dna chips 16S rRNA tree of life

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Genetic contributions to the study of taxonomy, ecology, and evolution of mayflies (Ephemeroptera): review and future perspectives

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AQUATIC INSECTS 2009年第sup1期31卷 19-39页

作者： Monaghan, Michael T. Sartori, Michel Leibniz Inst Freshwater Ecol & Inland Fisheries I Berlin Germany Museum Zool Lausanne Switzerland

Since the late 1970s, allozymes, microsatellites, and dna sequence variation have been widely used to Study the taxonomy, ecology, and evolution of mayflies (Ephemeroptera). Early research investigated species limits in morphologically cryptic groups and attempted to link immature and adult stages using genetic markers. Population genetic studies soon followed, with a strong emphasis on measuring gene flow as a proxy for dispersal. Most recently, direct sequencing of dna and molecular phylogenetic tools have broadened our understanding of mayfly systematics and evolution. Interestingly, these newer approaches have also begun to re-address some of the earliest questions about species circumscription and taxonomy. Here we present an overview of genetics in mayfly research to date, focusing on how genetic approaches have been applied to taxonomy, phylogenetics, and population genetics. We identify a number of outstanding questions and highlight some of the most interesting topics for future research. these include the need for evolutionarily valid species concepts when applying genetics to taxonomy, a better understanding of how parthenogenesis may affect population genetic structure, and increased use of dna sequence data from nuclear gene regions.

关键词： dispersal dna taxonomy heterozygosity mtdna phylogenetics population systematics

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Nucleosome positioning from tiling microarray data

Nucleosome positioning from tiling microarray data

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16th ISMB conference on Intelligent Systems for molecular Biology

作者： Yassour, Moran Kaplan, Tommy Jaimovich, Ariel Friedman, Nir Hebrew Univ Jerusalem Sch Comp Sci & Engn IL-91904 Jerusalem Israel Hebrew Univ Jerusalem Fac Med Dept Mol Biol & Biotechnol IL-91120 Jerusalem Israel

Motivation: the packaging of dna around nucleosomes in eukaryotic cells plays a crucial role in regulation of gene expression, and other dna-related processes. To better understand the regulatory role of nucleosomes, it is important to pinpoint their position in a high (5-10 bp) resolution. Toward this end, several recent works used dense tiling arrays to map nucleosomes in a high-throughput manner. these data were then parsed and hand-curated, and the positions of nucleosomes were assessed. Results: In this manuscript, we present a fully automated algorithm to analyze such data and predict the exact location of nucleosomes. We introduce a method, based on a probabilistic graphical model, to increase the resolution of our predictions even beyond that of the microarray used. We show how to build such a model and how to compile it into a simple Hidden Markov Model, allowing for a fast and accurate inference of nucleosome positions. We applied our model to nucleosomal data from mid-log yeast cells reported by Yuan et al. and compared our predictions to those of the original paper;to a more recent method that uses five times denser tiling arrays as explained by Lee et al.;and to a curated set of literature-based nucleosome positions. Our results suggest that by applying our algorithm to the same data used by Yuan et al. our fully automated model traced 13% more nucleosomes, and increased the overall accuracy by about 20%. We believe that such an improvement opens the way for a better understanding of the regulatory mechanisms controlling gene expression, and how they are encoded in the dna.

关键词： dna

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ProSOM:: core promoter prediction based on unsupervised clustering of dna physical profiles

ProSOM:: core promoter prediction based on unsupervised clus...

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16th ISMB conference on Intelligent Systems for molecular Biology

作者： Abeel, thomas Saeys, Yvan Rouze, Pierre Van de Peer, Yves Univ Ghent VIB Dept Plant Syst Biol B-9052 Ghent Belgium Univ Ghent Dept Mol Genet B-9052 Ghent Belgium Univ Ghent Lab Associe INRA B-9052 Ghent Belgium

Motivation: More and more genomes are being sequenced, and to keep up with the pace of sequencing projects, automated annotation techniques are required. One of the most challenging problems in genome annotation is the identification of the core promoter. Because the identification of the transcription initiation region is such a challenging problem, it is not yet a common practice to integrate transcription start site prediction in genome annotation projects. Nevertheless, better core promoter prediction can improve genome annotation and can be used to guide experimental work. Results: Comparing the average structural profile based on base stacking energy of transcribed, promoter and intergenic sequences demonstrates that the core promoter has unique features that cannot be found in other sequences. We show that unsupervised clustering by using self-organizing maps can clearly distinguish between the structural profiles of promoter sequences and other genomic sequences. An implementation of this promoter prediction program, called ProSOM, is available and has been compared with the state-of-the-art. We propose an objective, accurate and biologically sound validation scheme for core promoter predictors. ProSOM performs at least as well as the software currently available, but our technique is more balanced in terms of the number of predicted sites and the number of false predictions, resulting in a better all-round performance. Additional tests on the ENCODE regions of the human genome show that 98 of all predictions made by ProSOM can be associated with transcriptionally active regions, which demonstrates the high precision.

关键词： Forecasting

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MPLEM: An 80-processor FPGA Based Multiprocessor System

MPLEM: An 80-processor FPGA Based Multiprocessor System

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Annual IEEE Symposium on Field-Programmable Custom computing Machines (FCCM)

作者： Georgios-Grigorios Mplemenos Ioannis Papaefstathiou Department of Electronic and Computer Engineering Technical University of Crete Chania Greece

Multiprocessor embedded systems (MESes) are a very promising approach for high performance yet relatively low-cost computing. At the same time modern FPGAs provide the silicon capacity to build multiprocessor systems containing 10-100 processors, complex memory systems, heterogeneous interconnection schemes and custom engines executing the performance-critical operations. In this work we present a MES implemented in a state-of-the-art FPGA consisting of up to eighty 32-bit processors. the efficiency of our approach is demonstrated by the fact that our system can execute the BLAST CPU-intensive application, which is the prevalent tool used by molecular biologists for dna sequence matching and database search, many times faster than a simple PC.

关键词： Field programmable gate arrays Multiprocessing systems Embedded system Embedded computing High performance computing Silicon Engines dna Sequences Databases

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the algebraic computing structure of four dna bases

The algebraic computing structure of four DNA bases

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16th international conference on Artificial Reality and Telexistence - Workshops, ICAT 2006

作者： Zhu, Ping Tang, Xuqing Xu, Zhenyuan Guan, Weihong School of Science Southern Yangtze University Wuxi 214122 China Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University Hefei 230039 China

ISBN: (纸本)076952754X

In this paper, we offers a new algebraic point of view for dna molecules and introduce the algebraic system by using the natural operation based on the Σ = {A, C, G, T}. We characterize its structure by using the algebraic theory. We show that (L, ∠, ⊗) is the distribution lattice of rings with identical element. Furthermore, we generalize this result to the W ρ(V), a set which elements simulates the dna molecules with sticky ends, the element is called an incomplete double stranded molecules consist of mixed dna molecules with double and single strands. © 2006 IEEE.

关键词： dna

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