基于Spark的基因短序列比对模型

针对生物信息分析中基因短序列比对任务计算耗时长的问题,采用Spark平台、RDD数据集以及分布式文件系统HDFS设计了一种分布式计算模型。采用分而治之的策略将庞大的计算任务分割为多个互不重叠的小任务在分布式集群上并行执行。通过基于位置偏移量等分的数据分区算法实现数据的分发;通过将基因短序列封装入RDD数据集的方法实现了短序列的逐条处理;通过将基因比对算法传入RDD的Map函数的方法实现了基因序列的比对。计算模型的实现使得串行比对算法在分布式集群上可扩展,并显著降低了计算耗时,计算结果可与后续的生物信息分析工作相兼容。实验结果证明计算模型具有较好的稳定性和可扩展性,在Spark集群上取得了优秀的加速比。     

基于动态规划的Needleman-Wunsch双序列比对算法的分析与研究

生物序列比对是生物信息学中最基础的研究课题之一。基于动态规划的Needleman- Wunsch双序列比对算法主要采用迭代算法及空位罚分规则对基因序列进行逐一比对,计算二者相似性得分,最后通过回溯分析得出序列之间的最佳比对。虽然该算法可以得到最佳比对结果,但是时间复杂度和空间复杂度较高。首先对原算法进行分析,对计算得分和回溯进行改进。接着设计2次实验,以金黄色葡萄球菌和银葡萄球菌分别作为目标序列和待比对序列,分别生成序列长度范围相同和不同的5组数据进行实验测试。最后通过对新型冠状病毒和SARS病毒全序列进行比对,进一步验证了改进算法的有效性。实验结果表明,改进后的算法可以缩短序列比对时间,提高序列比对效率。     

基于遗传算法与星比对的多序列比对混合算法

多序列比对(MSA)是一个典型的NP完全问题，星比对是一种有效的多序列比对算法。文章针对MSA问题提出了将遗传算法与星比对算法结合在一起的混合算法，该算法充分发挥了遗传算法和星比对算法的优越性，可提高求解MSA问题的计算精度和计算速度，整个算法模拟了自然界进化的周期性，较好的解决了群体的多样性和收敛深度的矛盾。实验表明，该算法是有效的。     

渐进方法结合蚁群算法求解多序列比对问题

在所有多重序列比对算法中,渐进比对方法由于简单的算法和高效的计算在生物信息学中得到了广泛的应用。但是渐进方法最大的缺点是在早期阶段形成的错误不能在后期的计算中纠正过来。针对这个问题,我们设计了ProAnt比对算法,即渐进方法和蚁群算法相结合来求解多重序列比对问题。首先,对输入的多个序列进行预处理,用蚁群算法和概率一致性更新计算出所有字符对在最终比对中出现的概率,称为“后验概率”,计算后验概率是为了预防早期错误的发生。然后我们将后验概率作为字符对之间的匹配得分,用渐进方法得到最终的比对结果。用BAliBASE数据库对算法进行测试,实验结果显示,该算法能够在保持合理的运算时间的前提下显著改善渐进比对方法的正确性。     

生物多序列比对的并行算法

多序列比对是生物信息学中的基本问题。由于生物序列数据库的快速增长,即使优秀的串行算法已不能满足实际的需要。研究了Gusfield提出的星型比对模型的串行算法,进行了空间和时间上的改进,基于cluster结构的菜并行机提出了一种并行算法,并对大量基因数据进行了测试,结果表明对于大规模的多序列比对,算法能达到较高的加速比。     

一种新的迭代渐进多序列比对算法

该文提出一种新的迭代渐进多序列比对算法IPMSA。该算法先用渐进方法进行多序列比对,然后通过迭代策略,利用上一轮多序列比对结果修正指导树,产生新一轮比对。重复这一过程,直到指导树不再发生变化或满足事先设定的迭代次数为止。以比对数据库BAliBASE中多蛋白质家族1idy为例,对IPMSA算法和ClustalW算法进行的比较研究表明,该算法能更有效地比对分歧较大的序列,并改进其系统发育树。     

基于改进的蚁群算法的多序列比对

该文将蚁群算法进行了改进,将其应用于多序列比对,只根据信息素的强度对序列比对进行信息素强度的局部和全局动态更新,在避免了多序列比对容易陷入局部最优解的前提下,提高了收敛速度。同时,本算法应用在多序列比对中的最大优势是减少了传统算法在多序列比对问题中的生成系统树的步骤,减少了多序列比对过程的复杂度,在没有降低比对结果精确度的同时,提高了比对效率。     

一种优化的三序列比对算法及并行实现

序列比对算法在许多不同的领域得到应用。当前,一个重要的应用就是比对大分子,例如DNA和蛋白质序列比对。许多情况,有必要比对三序列。DavidR.Powell就提出过一种使用线性空位罚分的优化的三序列比对算法。这个算法最早是由Ukkonen提出的,该算法基于简单打分的两序列比对。该文通过引入“检查点法”对其进行改进,并充分利用近期蓬勃发展的高性能计算技术,对算法并行化,且在cluster机上实现。     

启发式序列比对算法种子长度及其灵敏度研究

序列比对是生物信息学中一个重要的研究方向,它可以确定两个或多个序列之间的相似性,进而判断其同源性并推测出序列间的进化关系。目前,启发式序列比对算法BLAST算法在实际问题用着重要应用。该算法中有一个参数叫做种子(Seeds),种子是控制比对速度和灵敏度的关键。但是种子的长度是基于经验而取的一个固定值,这个经验值并不适合于所有长度序列比对问题。因此,对于两条不用长度的序列之间实现启发式比对就需要取合理长度的种子,以便实现高效快速的比对。文中应用概率随机的思想对不同长度序列比对的种子的长度进行了分析,在此基础上对一定长度下种子的比对灵敏度做出了计算。通过理论推导和实验分析一定灵敏度下种子长度的计算结果是可行且有效的。这就给在高灵敏度(灵敏度几乎等于动态规划算法)下实现快速启发式序列比对的优化提供了保证。     

DNA双序列比对问题的算法

随着生物序列数据库中序列数据的激增, 开发兼有高度生物敏感性和高效率的算法显得极为迫切. 通过对生物序列比对问题中Needleman-Wunsch算法和Smith-Waterman算法深入分析, 提出了Smith-Waterman算法的改进算法, 并通过实验验证该算法, 对改进前后的运行性能进行比较分析. 实验证明, 改进后的算法实现了双序列局部最优解个数的优化, 有效降低了生物序列比对算法时间与空间的复杂性, 提高序列比对的得分率和准确率.     

煤矿井下安全监控分站的设计及其仿真实现

为了设计一种具有低成本、低功耗、易操作、功能强且可靠性高的煤矿井下安全分站,针对煤矿安全生产实际,文章提出了采用MCS-51系列单片机为核心、具有CAN总线通信接口的煤矿井下安全监控分站的设计方案;首先给出煤矿井下安全监控分站的整体构架设计,然后着重阐述模拟量输入信号处理系统的设计过程,最后说明单片机最小系统及其键盘、显示、报警、通信等各个组成部分的设计;为验证设计方案的可行性与有效性,使用Proteus软件对设计内容进行仿真验证,设计的煤矿井下安全监控分站具有瓦斯、温度等模拟量参数超标报警功能和电机开停、风门开闭等开关量指示功能;仿真结果表明:设计的煤矿井下安全监控分站具有一定的实际应用价值.     

Call for Papers The 6^th International Conference on Grid and Cooperative Computing

Recent years have seen rapid advances in various grid-related technologies, middleware, and applications. The GCC conference has become one of the largest scientific events worldwide in grid and cooperative computing. The 6th international conference on grid and cooperative computing (GCC2007) Sponsored by China Computer Federation (CCF),Institute of Computing Technology, Chinese Academy of Sciences (ICT) and Xinjiang University ,and in Cooperation with IEEE Computer Soceity ,is to be held from August 16 to 18, 2007 in Urumchi, Xinjiang, China.     

View-based model-driven architecture for enhancing maintainability of data access services

In modern service-oriented architectures, database access is done by a special type of services, the so-called data access services (DAS). Though, particularly in data-intensive applications, using and developing DAS are very common today, the link between the DAS and their implementation, e.g. a layer of data access objects (DAOs) encapsulating the database queries, still is not sufficiently elaborated, yet. As a result, as the number of DAS grows, finding the desired DAS for reuse and/or associated documentation can become an impossible task. In this paper we focus on bridging this gap between the DAS and their implementation by presenting a view-based, model-driven data access architecture (VMDA) managing models of the DAS, DAOs and database queries in a queryable manner. Our models support tailored views of different stakeholders and are scalable with all types of DAS implementations. In this paper we show that our view-based and model driven architecture approach can enhance software development productivity and maintainability by improving DAS documentation. Moreover, our VMDA opens a wide range of applications such as evaluating DAS usage for DAS performance optimization. Furthermore, we provide tool support and illustrate the applicability of our VMDA in a large-scale case study. Finally, we quantitatively prove that our approach performs with acceptable response times.     

A pragmatic multi-method investigation of discrepant technological events: Coping,attributions, and ‘accidental’ learning

Discrepant technological events or situations that entail a problem, a misunderstanding or a difficulty with the Information Technology (IT) being employed, are common in the workplace, and can lead to frustration and avoidance behaviors. Little is known, however, about how individuals cope with these events. This paper examines these events by using a multi-method pragmatic approach informed by coping theory. The results of two studies – a critical incident study and an experiment – serve to build and test, respectively, a theoretical model that posits that individuals use a variety of strategies when dealing with these events: they experience negative emotions, make external attributions, and adopt engagement coping strategies directed at solving the event, eventually switching to a disengagement coping strategy when they feel they have no control over the situation. Furthermore, users’ efforts may result in ‘accidental’ learning as they try to overcome the discrepant IT events through engagement coping. The paper ends with a discussion of the results in light of existing literature, future opportunities for research, and implications for practice.     

The Distributed Time-Triggered Simulation Scheme: Core Principles and Supporting Execution Engine

Distributed real-time simulation is a young technology field but its practice is under increasing demands. In recent years the author and his collaborators have been establishing a new approach called the distributed time-triggered simulation (DTS) scheme which is conceptually simple and easy to use but widely applicable. The concept was initiated in the course of developing a new-generation object-oriented real-time programming scheme called the time-triggered message-triggered object (TMO) programming scheme. Some fundamental issues inherent in distributed real-time simulation that were learned during recent experimental studies are discussed along with some approaches for resolving the issues. An execution engine developed to support both the TMOs engaged in control computation and the TMOs engaged in DTS is also discussed along with its possible extensions that will enable significantly larger-scale DTSs.     

Software-Konfigurationsmanagement in großen Softwareprojekten

Zusammenfassung Mit zunehmender Größe der Softwaresysteme verschärfen sich die für die Software-Herstellung typischen Probleme: Beherrschen großer Objektmengen, Erhalten der Systemkonsistenz, Kontrolle der ständigen Änderungseinflüsse und Gewährleisten einer langen Lebensdauer. Die Disziplin Konfigurationsmanagement bildet den methodischen Ansatz, diese Probleme besser zu beherrschen. Software-Konfigurationsmanagement faßt die Herstellung von Softwaresystemen als eine Abfolge von kontrollierten Änderungen an gesicherten Zwischen- und Endergebnissen auf. Dargestellt werden die Objekte und Funktionen des Software-Konfigurationsmanagements sowie die hierfür in großen Software-Projekten benötigten Methoden, Instanzen und Hilfsmittel.     

Information for Authors

正http://www.zju.edu.cn/jzus http://www.springerlink.com Aim The Journals of Zhejiang University-SCIENCE(A/B/C)are edited by the international board of distinguished Chinese and foreign scientists,and are aimed to present the latest developments and achievements in scientific research in China and     

Editorial:Brain-machine interface(BMI) and cyborg intelligence

正Brain-machine interfaces(BMIs)aim at building a direct communication pathway between the brain and an external device,and represent an area of research where significant progress has been made during the past decade.Based on BMIs,mind information can be read out by neural signals to control     

Information for Authors

正http://www.zju.edu.cn/jzus http://www.springerlink.com Aim The Journals of Zhejiang University-SCIENCE(A/B/C)are edited by the international board of distinguished Chinese and foreign scientists,and are aimed to present the latest developments and achievements in scientific research in China and overseas to the world’s scientific circles,especially to stimulate     

SCIENCE CHINA Information Sciences SUBJECT INDEX TO VOLUME 57(2014)

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