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GTZ: a fast compression and cloud transmission tool optimized for FASTQ files

BMC BIOINFORMATICS 2017年第Sup16期18卷 549-549页

作者： Xing, Yuting Li, Gen Wang, Zhenguo Feng, Bolun Song, Zhuo Wu, Chengkun Genetalks Biotech Co Ltd Beijing 100000 Peoples R China Natl Univ Def Technol Sch Comp Sci Changsha 410000 Hunan Peoples R China

Background: the dramatic development of dna sequencing technology is generating real big data, craving for more storage and bandwidth. To speed up data sharing and bring data to computing resource faster and cheaper, it is necessary to develop a compression tool than can support efficient compression and transmission of sequencing data onto the cloud storage. Results: this paper presents GTZ, a compression and transmission tool, optimized for FASTQ files. As a reference-free lossless FASTQ compressor, GTZ treats different lines of FASTQ separately, utilizes adaptive context modelling to estimate their characteristic probabilities, and compresses data blocks with arithmetic coding. GTZ can also be used to compress multiple files or directories at once. Furthermore, as a tool to be used in the cloud computing era, it is capable of saving compressed data locally or transmitting data directly into cloud by choice. We evaluated the performance of GTZ on some diverse FASTQ benchmarks. Results show that in most cases, it outperforms many other tools in terms of the compression ratio, speed and stability. Conclusions: GTZ is a tool that enables efficient lossless FASTQ data compression and simultaneous data transmission onto to cloud. It emerges as a useful tool for NGS data storage and transmission in the cloud environment. GTZ is freely available online at: https://***/Genetalks/gtz.

关键词： FASTQ Compression General-purpose Lossless Parallel compression and transmission Cloud computing

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the Co-design of Astrophysical Code for Massively Parallel Supercomputers 16th

The Co-design of Astrophysical Code for Massively Parallel S...

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16th international conference on Algorithms and Architectures for Parallel Processing (ICA3PP)

作者： Glinsky, Boris Kulikov, Igor Chernykh, Igor Weins, Dmitry Snytnikov, Alexey Nenashev, Vladislav Andreev, Andrey Egunov, Vitaly Kharkov, Egor Inst Computat Math & Math Geophys SB RAS Lavrentjeva Ave 6 Novosibirsk 630090 Russia Novosibirsk State Tech Univ Novosibirsk 630073 Russia Volgograd State Tech Univ Volgograd 400005 Russia

ISBN: (纸本)9783319499567;9783319499550

the rapid growth of supercomputer technologies became a driver for the development of natural sciences. Most of the discoveries in astronomy, in physics of elementary particles, in the design of new materials in the dna research are connected with numerical simulation and with supercomputers. Supercomputer simulation became an important tool for the processing of the great volume of the observation and experimental data accumulated by the mankind. Modern scientific challenges put the actuality of the works in computer systems and in the scientific software design to the highest level. the architecture of the future exascale systems is still being discussed. Nevertheless, it is necessary to develop the algorithms and software for such systems right now. It is necessary to develop software that is capable of using tens and hundreds of thousands of processors and of transmitting and storing of large volumes of data. In the present work the technology for the development of such algorithms and software is proposed. As an example of the use of the technology, the process of the software development is considered for some problems of astrophysics.

关键词： Exascale systems Co-design High performance computing Computational astrophysics Physics of plasmas

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Simultaneous detection of multiple charged particles using a borosilicate nanopore-based sensor

Simultaneous detection of multiple charged particles using a...

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IEEE conference on Nanotechnology

作者： Yuqian Zhang Leyla Esfandiari Department of electrical and computing system University of Cincinnati Cincinnati OH Department of electrical and computing system University of Cincinnati Cincinnati OH USA

Nanopore sensing has been widely researched owing to its single molecule sensitivity. In this work, we have demonstrated the potential application of a relatively low-cost single borosilicate nanopore-based sensor for... 详细信息

关键词： Nanobioscience Sensors Multiplexing dna Glass Microscopy Proteins

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Challenges in the Reliability of 3D Integration using TSVs 16

Challenges in the Reliability of 3D Integration using TSVs

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16th IEEE international conference on thermal, Mechanical and Multiphysics Simulation and Experiments in Microelectronics and Microsystems (EuroSimE)

作者： Stiebing, M. Vogel, D. Steller, W. Wolf, M. J. Wunderle, B. Tech Univ Chemnitz Lehrstuhl Werkstoffe & Zuverlassigkeit Mikrotech Reichenhainer Str 70 D-09126 Chemnitz Germany Fraunhofer ENAS Micromat Ctr MMC D-09126 Chemnitz Germany Fraunhofer IZM ASSID D-01468 Moritzburg Germany

ISBN: (纸本)9781479999507

One of the possible target applications of 3D-integration is the high performance computing (HPC). the improved performance of 3D-integrating can base on an Interposer with heterogeneous integration of special high performance fluidic cooling, individual power supply next to the microprocessor and a tailored packaging approach. this paper focuses on the reliability assessment of the interposer regarding the interaction of TSV, wiring and fluid channel integration based on current publications in correlation with the selected specifications for Interposer manufacturing. A further part is the correlation with initial results of stress simulation and measurements applied to the Interposer design specifications of cavities and interconnect features (used for sealing the cooling channels and as electrical interconnect). We give an overview of a new level of complexity of 3D integration and discuss certain failure mechanisms that can influence the performance of 3D integrated devices. We show that the prediction of failure locations becomes possible by the method of finite element modeling but with the necessity to obtain process specific material data as an input for the simulation. An overview shows the possibilites of residual stresses analyses on test vehicles by using special methods of Raman spectroscopy and fibDAC including interpretation challenges of gathered measurement data. Furthermore the application of a new method for fatigue testing is proposed and discussed.

关键词： Raman spectrometry dna Integration integration Finite element method reliability evaluation Failure mechanisms Test vehicles High Performance computing material data Fatigue tests macroprocessor measurement data

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Support for bioinformatics applications through volunteer and scalable computing frameworks 16

Support for bioinformatics applications through volunteer an...

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16th IEEE international conference on Cluster computing (CLUSTER)

作者： Gutierrez, Felipe Azevedo, Danilo Barreto, Marcos Zucoloto, Rodrigo Fed Univ Bahia UFBA Comp Sci Dept Distributed Syst Lab LaSiD BR-40110170 Salvador BA Brazil Fed Univ Bahia UFBA Inst Biol Populat Genet & Mol Evolut Lab GENEV BR-40110170 Salvador BA Brazil

ISBN: (纸本)9781479955480

Many e-science applications can benefit from the elasticity of resources provided by volunteer and distributed platforms. While the former is based on resources assigned voluntarily by its owners, the second is based on resources specially configured for this purpose. In this paper, we present the integration of BOINC and Hadoop, two of the most popular middlewares available today, at the infrastructure level of mc(2), a platform designed to support scientific applications. We discuss some case studies related to dna sequencing running in Cloud-Burst, model selection running in the MEGA Computational Core and similarity searches running in BLAST. Our results show scientific users can run their experiments in our platform with a high level of abstraction and, in some cases, with very good performance.

关键词： bioinformatics cloud computing grid computing middleware BLAST BOINC Cloud-Burst dna sequencing Hadoop MEGA computational core e-science scalable computing framework volunteer computing framework Bioinformatics Computational modeling dna Middleware Portals Servers

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dna computing and molecular programming - 16th international conference, dna 16, Revised Selected Papers

DNA Computing and Molecular Programming - 16th International...

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16th international conference on dna computing and molecular programming, dna 16

ISBN: (纸本)9783642183041

the proceedings contain 16 papers. the topics discussed include: improving efficiency of 3-SAT-solving tile systems;optimizing tile concentrations to minimize errors and time for dna tile self-assembly systems;scalable, time-responsive, digital, energy-efficient molecular circuits using dna strand displacement;negative interactions in irreversible self-assembly;search and validation of short genome-wide biomarkers for bacterial biological phylogenies;high-fidelity dna hybridization using programmable molecular dna devices;synthesizing minimal tile sets for patterned dna self-assembly;operation of a dna-based autocatalytic network in serum;triangular tile self-assembly systems;randomized self assembly of rectangular nano structures;design of a functional nanomaterial with recognition ability for constructing light-driven nanodevices;efficient Turing-universal computation with dna polymers;and simple evolution of complex crystal species.

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SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi Coprocessors for Long dna Sequences 16

SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi Coprocessors...

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16th IEEE international conference on Cluster computing (CLUSTER)

作者： Liu, Yongchao Tran, Tuan-Tu Lauenroth, Felix Schmidt, Bertil Johannes Gutenberg Univ Mainz Inst Informat Mainz Germany

ISBN: (纸本)9781479955480

As an optimal method for sequence alignment, the Smith-Waterman (SW) algorithm is widely used. Unfortunately, this algorithm is computationally demanding, especially for long sequences. this has motivated the investigation of its acceleration on a variety of high-performance computing platforms. However, most work in the literature is only suitable for short sequences. In this paper, we present SWAPHI-LS, the first parallel SW algorithm exploiting emerging Xeon Phi coprocessors to accelerate the alignment of long dna sequences. In SWAPHI-LS, we have investigated three parallelization approaches (naive, tiled, and distributed) in order to deeply explore the inherent parallelism within Xeon Phis. To achieve high speed, we have explored two levels of parallelism within a single Xeon Phi and one more level of parallelism between Xeon Phis. Within a single Xeon Phi we exploit instruction-level parallelism within 512-bit single instruction multiple data (SIMD) instructions (vectorization) as well as thread-level parallelism over the many cores (multi-threading). Between Xeon Phis we employ device-level parallelism in order to harness the compute power of Xeon Phi clusters (distributed computing based on the MPI offload model). the performance of our algorithm has been evaluated using a variety of genome sequences of lengths ranging from 4.4 million to 50 million nucleotides. Our performance evaluation reveals that our implementation achieves a stable performance of up to 30.1 billion cell updates per second (GCUPS) on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing the same host. SWAPHI-LS is written in C++ (with a set of SIMD intrinsics), OpenMP and MPI. the source code is publicly available at http://***.

关键词： dna sequences

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Practical Aspects of Declarative Languages - 16th international Symposium, PADL 2014, Proceedings

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15th international conference on Verification, Model Checking, and Abstract Interpretation, VMCAI 2014

ISBN: (纸本)9783319041315

the proceedings contain 15 papers. the topics discussed include: partial type signatures for Haskell;abstract modular inference systems and solvers;sunroof: a monadic DSL for generating JavaScript;compiling dna strand displacement reactions using a functional programming language;two applications of the ASP-prolog system: decomposable programs and multi-context systems;towards modeling morality computationally with logic programming;a declarative specification of giant number arithmetic;embedding foreign code;on the correctness and efficiency of lock-free expandable tries for tabled logic programs;typelets - a rule-based evaluation model for dynamic, statically typed user interfaces;expand: towards an extensible pandoc system;and generic generic programming.

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2014 IEEE international conference on Cluster computing, CLUSTER 2014

2014 IEEE International Conference on Cluster Computing, CLU...

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16th IEEE international conference on Cluster computing, CLUSTER 2014

ISBN: (纸本)9781479955480

the proceedings contain 60 papers. the topics discussed include: scalable replay with partial-order dependencies for message-logging fault tolerance;applying frequency analysis techniques to DAG-based workflows to benchmark and predict resource behavior on non-dedicated clusters;memory management for billions of small objects in a distributed in-memory storage;software technologies coping with memory hierarchy of GPGPU clusters for stencil computations;disk cache-aware task scheduling for data-intensive and many-task workflow;scalable graph500 design with MPI-3 RMA;SWAPHI-LS: Smith-Waterman algorithm on xeon phi coprocessors for long dna sequences;boosting the performance of remote GPU virtualization using InfiniBand connect-IB and PCIe 3.0;leveraging deep memory hierarchies for data staging in coupled data-intensive simulation workflows;and load analysis and cost estimation of parallel constrained producer-consumer algorithms.

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High Performance Genomic Sequencing: A Filtered Approach 8

High Performance Genomic Sequencing: A Filtered Approach

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8th international conference on Practical Applications of Computational Biology & Bioinformatics (PACBB)

作者： Retamosa, German de Pedro, Luis Gonzalez, Ivan Tamames, Javier Univ Autonoma Madrid High Performance & Comp Networking Dept E-28049 Madrid Spain CSIC Natl Biotechnol Res Ctr Madrid Spain

ISBN: (纸本)9783319075815;9783319075808

Protein and dna homology detection systems are an essential part in computational biology applications. these algorithms have changed over the time from dynamic programming approaches by finding the optimal local alignment between two sequences to statistical approaches with different kinds of heuristics that minimize former executions times. However, the continuously increasing size of input datasets is being projected into the use of High Performance computing (HPC) hardware and software in order to address this problem. the aim of the research presented in this paper is to propose a new filtering methodology, based on general-purpose graphical processor units (GP-GPUs) and multi-core processors, for removing those sequences considered irrelevant in terms of homology and similarity. the proposed methodology is completely independent from the homology detection algorithm. this approach is very useful for researchers and practitioners because they do not need to understand a new algorithm. this design has been approved by the National Biotechnology Research Center of Spain (CNB).

关键词： Comparison and alignment methods BLAST High Performance computing GP-GPU

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