检索结果-内蒙古大学图书馆

Agile parallel bioinformatics workflow management using Pwrake

BMC Research Notes 2011年第1期4卷 1-8页

作者： Mishima, Hiroyuki Sasaki, Kensaku Tanaka, Masahiro Tatebe, Osamu Yoshiura, Koh-Ichiro Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 1-12-4 Sakamoto Japan Nagasaki University Global Center of Excellence Program Nagasaki Nagasaki 1-12-4 Sakamoto Japan Center for Computational Sciences University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan Core Research for Evolutional Science and Technology Japan Science and Technology Agency Kawaguchi Saitama 4-1-8 Honcho Japan Departmentent of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan

Background: In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions: Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

关键词： Ruby Iterative Development Agile Software Development Host Language Bioinformatics Domain

来源：评论

学校读者我要写书评

暂无评论

Low-frequency 1/f noise in bismuth selenide Topological Insulators

Low-frequency 1/f noise in bismuth selenide Topological Insu...

引用

International Conference on Noise and Fluctuations (ICNF)

作者： M. Z. Hossain K. M. F. Shahil D. Teweldebrhan A. A. Balandin S. L. Rumyantsev M. Shur Nano-Device Laboratory Department of Electrical Engineering and Materials Science and Engineering Program University of California Riverside CA USA Department of Electrical Computer and Systems Engineering and Center for Integrated Electronics Rensselaer Polytechnic Institute New York USA Ioffe Institute The Russian Academy of Sciences St. Petersburg Russia

ISBN: (纸本)9781457701894

Topological insulators is a newly discovered class of materials with the Dirac cone type dispersion at the surface and conventional band in the volume of the material. We present results of the study of the low-frequency excess noise in thin films made of Bi 2 Se 3 topological insulator material. The films were prepared through mechanically cleavage from the bulk crystal via the “graphene-like” exfoliation procedure. We verified the quality and crystallinity of Bi 2 Se 3 samples with the micro-Raman spectroscopy. Our fabricated devices have linear current voltage characteristics in the low bias region with the current fluctuation noise spectral density SI proportional to 1/f for frequency f less than 10 kHz. The noise spectral density SI showed the square law dependence on the source-drain current and changed from about ~10 -22 to 10 -18 A 2 /Hz as current changes form ~10 -7 to 10 -5 A. Our results can be used for understanding electron transport and trap dynamics, and for reducing low-frequency noise in topological insulator devices.

关键词： Noise Insulators Films Crystals Temperature measurement Resistance

来源：评论

学校读者我要写书评

暂无评论

Microfluidic flow cytometer utilizing optical space-time coding technique

Microfluidic flow cytometer utilizing optical space-time cod...

引用

IEEE Photonics Conference (IPC)

作者： Tsung-Feng Wu Zhe Mei Luca Pion-Tonachini Yu-Hwa Lo Materials Science and Engineering Program University of California at San Diego La Jolla CA USA School of Information and Electronics Beijing Institute of Technology Beijing China Department of Electrical and Computer Engineering University of California at San Diego La Jolla CA USA

An optical-coding technique for microfluidic flow cytometers to detect forward scattering and large angle scattering signals that can be used to differentiate beads and cells.

关键词： Optical scattering Microfluidics Optical sensors Optical signal processing Optical device fabrication Biomedical optical imaging

来源：评论

学校读者我要写书评

暂无评论

A Parallel Ray Tracing Architecture Suitable for Application-Specific Hardware and GPGPU Implementations

A Parallel Ray Tracing Architecture Suitable for Application...

引用

Euromicro Symposium on Digital System Design

作者： Alexandre S. Nery Nadia Nedjah Felipa M.G. Franca Lech Jozwiak LAM-Computer Architecture and Microelectronics Laboratory Systems Engineering and Computer Science Program COPPE Universidade Federal do Rio de Janeiro Brazil Department of Electrical Engineering-Electronic Systems Eindhoven University of Technology Netherlands Universidade do Estado do Rio de Janeiro Rio de Janeiro RJ BR

The Ray Tracing rendering algorithm can produce high-fidelity images of 3-D scenes, including shadow effects, as well as reflections and transparencies. This is currently done at a processing speed of at most 30 frames per second. Therefore, actual implementations of the algorithm are not yet suitable for interactive real-time rendering, which is required in games and virtual reality based applications. Fortunately, the algorithm allows for massive parallelization of its computations. In this paper, we present a parallel architecture for ray tracing based on a uniform spatial subdivision of the scene and exploiting an embedded computation of ray-triangle intersections. This approach allows for a significant acceleration of intersection computations, as well as, a reduction of the total number of the required intersections checks. Furthermore, it allows for these checks to be performed in parallel and in advance for each ray. In this paper we discuss and analyze an ASIP-based implementation using FPGAs and a GPGPU-based parallel implementation of the proposed architecture. The performance of both implementations are reported and compared.

关键词： Ray tracing Graphics processing unit Instruction sets computer architecture Registers Image color analysis Hardware

来源：评论

学校读者我要写书评

暂无评论

Evaluation of an Intelligent Fuzzy-Based Cluster Head Selection System for WSNs Using Different Parameters

Evaluation of an Intelligent Fuzzy-Based Cluster Head Select...

引用

International Conference on Advanced Information Networking and Applications Workshops (AINAW)

作者： Leonard Barolli Hironori Ando Fatos Xhafa Arjan Durresi Rozeta Miho Akio Koyama Department of Information and Communication Engineering Fukuoka Institute of Technology Fukuoka Japan Graduate School of Engineering Fukuoka Institute of Technology Fukuoka Japan Department of Languages and Informatics Systems Technical University of Catalonia Barcelona Spain Department of Computer and Information Science Purdue University Indiana University Indianapolis IN USA Department of Electronics and Telecommunication Polytechnic University of Tirana Tirana Albania Department of Informatics Yamagata University Yonezawa Yamagata Japan

Cluster formation and cluster head selection are important problems in sensor network applications and can drastically affect the network's communication energy dissipation. However, selecting of the cluster head is not easy in different environments which may have different characteristics. In our previous work, in order to deal with this problem, we proposed a power reduction algorithm for sensor networks based on fuzzy logic and number of neighbour nodes. We call this algorithm F3N. In this paper, we evaluate F3N and LEACH by many simulation results. We evaluate the performance of our proposed system for tree different parameters: Remaining Battery Power of Sensor (RPS), Degree of Number of Neighbour Nodes (D3N), and Distance from Cluster Centroid (DCC). From the simulation results, we found that the probability of a sensor node to be a cluster head is increased with increase of number of neighbour nodes and remained battery power and is decreased with the increase of distance from the cluster centroid.

关键词： Clustering algorithms Simulation Mercury (metals) Manganese Fuzzy logic Batteries Electronic mail

来源：评论

学校读者我要写书评

暂无评论

Metamorphic solar cells employing chemical mechanical polishing and MOVPE regrowth

Metamorphic solar cells employing chemical mechanical polish...

引用

2011 37th IEEE Photovoltaic Specialists Conference

作者： L. J. Mawst P. Dudley J. Kirch T. Kim S. Ruder T. F. Kuech R. Tatavarti Department of Electrical and Computer Engineering University of Wisconsin-Madison Madison WI USA Materials Science Program University of Wisconsin-Madison Madison WI USA Department of Chemical and Biological Engineering University of Wisconsin-Madison Madison WI USA Microlink Devices Inc. Niles IL USA

We have investigated the MOVPE growth of In x Ga 1-x As metamorphic buffer layer (MBL) structures with a focus on techniques to improve the surface morphology and determine the influence of morphology on subsequently grown single-junction device structures. To improve the surface roughness of the underlying MBL, Chemical-Mechanical Polishing (CMP) is employed and MOVPE regrowth of single-junction (SJ) solar cells on top of the polished surface is performed. AFM image analysis indicates the CMP process is effective in reducing the step-graded In x Ga 1-x As MBL surface roughness from ~7-10 nm (as-grown) to 2.3 nm post CMP. A post-CMP ozone/HF treatment was found to be effective in removing silica residue remaining on the surface from the CMP process, allowing for the growth of films on top of the MBL surface subjected to CMP. Improved short circuit current density (J sc ) and external quantum efficiency (QE) were obtained from SJ (1eV) devices which employ the CMP process compared with those on as-grown MBLs.

关键词： Surface roughness Rough surfaces Surface treatment Surface morphology Indium gallium arsenide Epitaxial layers Epitaxial growth

来源：评论

学校读者我要写书评

暂无评论

Supervised Learning Framework For Screening Nuclei in Tissue Sections

Supervised Learning Framework For Screening Nuclei in Tissue...

引用

Annual International Conference of the IEEE engineering in Medicine and Biology Society

作者： Kaustav Nandy Prabhakar R. Gudla Ryan Amundsen Karen J. Meaburn Tom Misteli Stephen J. Lockett Optical Microscopy and Analysis Laboratory Advanced Technology program SAIC-Frederick Inc. Electrical Engineering and Computer Science Department University of Michigan Cell Biology of Gene Expression National Cancer Institute National Institutes of Health

ISBN: (纸本)9781424441211

Accurate segmentation of cell nuclei in microscope images of tissue sections is a key step in a number of biological and clinical applications. Often such applications require analysis of large image datasets for which manual segmentation becomes subjective and time consuming. Hence automation of the segmentation steps using fast, robust and accurate image analysis and pattern classification techniques is necessary for high throughput processing of such datasets. We describe a supervised learning framework, based on artificial neural networks (ANNs), to identify well-segmented nuclei in tissue sections from a multistage watershed segmentation algorithm. The successful automation was demonstrated by screening over 1400 well segmented nuclei from 9 datasets of human breast tissue section images and comparing the results to a previously used stacked classifier based analysis framework.

关键词： tissue section Cell nucleus Semi-supervised Learning Nucleus Dataset image analysis MULTISTAGE Artificial neural networks Frameworks nuclei (nuclear physics) segmentation Segmentation Automation pattern classification method

来源：评论

学校读者我要写书评

暂无评论

Characteristics of low latitude nocturnal ionospheric irregularities over India-Arab longitudes during solar maximum

Characteristics of low latitude nocturnal ionospheric irregu...

引用

General Assembly and Scientific Symposium, URSI

作者： Fang-Dar Chu Wei-Sheng Chen Chien-Chih Lee Wei-Chih Hsu Huang-Tien Lin Chia-Shu Liao National Standard Time and Frequency Laboratory of Telecommunication Laboratories Chunghwa Telecom Company Limited Yangmei Taoyuan Taiwan General Education Center Ching Yun University Zhongli Taoyuan Taiwan Department of Computer and Communication Engineering National Kaohsiung First University of Science and Technology Kaohsiung Taiwan

This study investigated the low latitude nocturnal ionospheric irregularities at India-Arab longitudes using phase fluctuations of the global positioning system during solar maximum. The results showed that the low latitude irregularities in this region develop easier in equinoctial months and December-solstice months than in June-solstice months. In addition, the low latitude irregularities mainly come from the magnetic equator. Moreover, at the crest of equatorial anomaly the irregularities in June-solstice months maybe come from middle latitudes. Many details are discussed.

关键词： Global Positioning System Fluctuations Cities and towns Satellites Ionosphere Satellite broadcasting Time frequency analysis

来源：评论

学校读者我要写书评

暂无评论

A load balancing data gathering scheme in wireless sensor networks with mobile sinks

A load balancing data gathering scheme in wireless sensor ne...

引用

2010 6th International Conference on Wireless Communications, Networking and Mobile Computing, WiCOM 2010

作者： Lin, Lin Yan, Shu Yi, Nian Department of Computer Science and Telecommunication Engineering Jiangsu University Zhenjiang China

ISBN: (纸本)9781424437092

The existing data gathering scheme in wireless sensor networks usually takes place from sensors to static sinks. If sink can move randomly, data gathering process needs the cooperation of sinks. In this article, a load balancing data gathering scheme is proposed. In our scheme, the sensed data for target is stored in the storage path pointed to the network center, and the query request put forward by the mobile sink is transmitted along the circle whose center is the network center. Sensed information and query information match in a sensor node. The simulation results manifest that the proposed method can balance the energy load efficiently and prolong the network lifetime. © 2010 IEEE.

关键词： Sensor nodes

来源：评论

学校读者我要写书评

暂无评论

A travel time prediction method: Bayesian reasoning state-space neural network

A travel time prediction method: Bayesian reasoning state-sp...

引用

2nd International Conference on Information science and engineering, ICISE2010

作者： Li, Xingyi Wang, Cunqing Shi, Huaji Department of Computer Science and Telecommunication Engineering Jiangsu University Zhenjiang China

ISBN: (纸本)9781424480968

According to the prediction model of neural network training methods to slow convergence speed, training for a long time and difficult to control the complexity of weights updating, this paper puts forward Bayesian reasoning state-space neural network, using termination conditions control its training and the confidence interval restrained by control factor standard the results. Using this method can accelerate convergence, shorten the training time and maintain stability. With traffic data by Bin He road of Shenzhen in September 2007 to verify this model, the experiments show that this model can shorten the time of training, and has good robustness and accuracy. © 2010 IEEE.

关键词： Bayesian networks

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：