CUDA-TP:基于GPU的自顶向下完整蛋白质鉴定并行算法

蛋白质及蛋白质翻译后修饰(post-translational modifications, PTMs)的鉴定是蛋白质组学研究的基础,对整个领域的进一步发展有着十分重要的意义.近年来,质谱设备的快速发展使得获取“自顶向下”(top-down,TD)的高精度完整蛋白质质谱数据成为可能.目前基于TD质谱数据的完整蛋白质鉴定算法虽然在匹配精度、PTM位点的推断上取得了一些成效,但它们运行时间还有很大的不足和提升空间.利用图形处理器(graphics processing unit, GPU)可以将大规模的重复计算并行化,提高串行程序的执行速度.CUDA-TP算法基于通用并行计算架构(compute unified device architecture, CUDA)来计算蛋白质与TD质谱数据的匹配分数.首先,对每一个质谱数据,CUDA-TP利用优化的MS-Filter算法在蛋白质数据库中过滤出其对应的少数候选蛋白质集合,然后通过AVL(adelson-velskii and landis)树加速质谱匹配过程.GPU中的多线程技术被用来并行化谱图网格及最终数组中所有元素的前驱结点的求解.同时,该算法还使用target-decoy策略来控制蛋白质与质谱图匹配结果的错误发现率(false discovery rate, FDR).实验结果表明：CUDA-TP算法能够有效地加速完整蛋白质的鉴定,速度分别比MS-TopDown和MS-Align+快10倍与2倍.到目前为止,这是唯一能够利用CUDA架构来加速完整蛋白质鉴定的研究工作.CUDA-TP源代码公布在https://github.com/dqiong/CUDA-TP.     

Memoing Evaluation for Constraint Extensions of Datalog

This paper proposes an efficient method for evaluation of deductive queries over constraint databases. The method is based on a combination of the top-down resolution with memoing and the closed form bottom-up evaluation. In this way the top-down evaluation is guaranteed to terminate for all queries for which the bottom-up evaluation terminates. The main advantage of the proposed method is the direct use of the information present in partially instantiated queries without the need for rewriting of the original program. The evaluation algorithm automatically propagates the necessary constraints during the computation. In addition, the top-down evaluation potentially allows the use of compilation techniques, developed for compilers of logic programming languages, which can make the query evaluation very efficient.     

Study on Top-Down Estimation Method of Software Project Planning

1Foreword Allprojectmanagementwillbeginwithprojectplan ning.Theprojectplanproducedbyprojectplanningis themostimportanttooltocoordinatetheprojectwork effectively,andmaketheprojectworkimplemented successfully.Onlybyeffectiveprojectplanning,could wemakeeffec…     

基于NX参数化自顶向下的设计方法及其在减速器中的应用

介绍了自顶向下的设计方法,并且在NX中利用自顶向下的方法对减速器进行了设计,将自顶向下方法和NX参数化相结合,通过建立减速器的控制结构,实现了减速器的整体结构控制;利用NX的wave功能和“表达式”功能实现了参数的逐级传递、各零件参数之间的关联、零部件的并行设计和自动化装配.     

基于骨架模型的船体结构快速建模

针对当前我国船舶结构设计中迭代次数多、设计存在异地性的问题,提出一种船 体结构快速建模方法。以“自顶向下”为设计思路,以骨架模型为实现载体,对船体结构特点进 行分析、总结后构建了面向船舶结构的骨架模型,给出船体结构骨架模型的定义。通过船舶结 构的骨架模型与参数坐标系实现船舶总体的快速布局设计;建立参数坐标系与船体板架之间的 关联关系实现船体结构的快速建模与快速调整,并给出相应算法;给出设计信息的组织方式并 将设计信息集成到骨架模型实现船体结构模型的完整性定义与快速建立。最后基于 CATIA V6 平台开发快速建模系统,并通过纵骨架式船体结构验证了方法的可行性。     

不同开挖方式对软土区深基坑连续墙变形的影响分析

以上海地区某地下变电站深基坑工程为背景,根据工程实测数据分析基坑开挖对支护结构变形的影响规律。结果表明:基坑开挖过程中,连续墙的位移呈抛物线形,且位移值随着开挖深度增加而增加,但最大水平位移的位置始终保持在开挖面附近;基坑支护结构的变形受到明显的坑角效应影响。采用有限元软件Plaxis分别对该工程顺作法和逆作法施工过程进行数值模拟,通过分析比较得出不同施工方案对基坑变形的影响规律。将数值模拟结果与实测数据对比,分析逆作法施工方案的可行性与优势。     

异地分布式存储环境下的产品数据一致性控制技术

为了解决分布存储机制所带来的产品数据一致性问题，依据产品数据的产生位置和使用属性，设计了基于主副本的产品数据分布存储策略，同时，在异地企业间设计并使用了主一辅服务器协同的并行处理机制。通过基于数据全相关的产品数据一致性更新技术，解决了异地产品数据之间的主副本一致性实时更新问题；通过基于自顶向下的产品数据一致性检查技术，实现了盟主企业的产品中心数据库和联盟企业的产品次级数据库的主动核对和自动检查。两种一致性控制策略的协同工作，较好地解决了产品数据异地分布式存储环境下的一致性控制问题，并以航空某企业联盟为应用背景，进行了应用验证。     

Top-down causation by information control: from a philosophical problem to a scientific research programme.

It has been claimed that different types of causes must be considered in biological systems, including top-down as well as same-level and bottom-up causation, thus enabling the top levels to be causally efficacious in their own right. To clarify this issue, the important distinctions between information and signs are introduced here and the concepts of information control and functional equivalence classes in those systems are rigorously defined and used to characterize when top-down causation by feedback control happens, in a way that is testable. The causally significant elements we consider are equivalence classes of lower level processes, realized in biological systems through different operations having the same outcome within the context of information control and networks.     

State of the Art and Perspectives of Hierarchical Zeolites: Practical Overview of Synthesis Methods and Use in Catalysis

Microporous zeolites have proven to be of great importance in many chemical processes. Yet, they often suffer from diffusion limitations causing inefficient use of the available catalytically active sites. To address this problem, hierarchical zeolites have been developed, which extensively improve the catalytic performance. There is a multitude of recent literature describing synthesis of and catalysis with these hierarchical zeolites. This review attempts to organize and overview this literature (of the last 5 years), with emphasis on the most important advances with regard to synthesis and application of such zeolites. Special attention is paid to the most common and important 10- and 12-membered ring zeolites (MTT, TON, FER, MFI, MOR, FAU, and *BEA). In contrast to previous reviews, the research per zeolite topology is brought together and discussed here. This allows the reader to instantly find the best synthesis method in accordance to the desired zeolite properties. A summarizing graph is made available to enable the reader to select suitable synthesis procedures based on zeolite acidity and mesoporosity, the two most important tunable properties.     

基于Pro/Engineer的虚拟设计方法研究

传统的产品设计都是在产品设计完成之后进行试装配,对不满足要求的零部件进行重新设计。介绍了Pro/Engineer的实体造型及虚拟装配的特点,并分析了自顶向下和自底向上两种设计思路,根据复杂装置设计的具体特点,构建了虚拟环境下产品设计的基本流程。实践证明,基于Pro/Engineer的虚拟装配设计方法能提前发现设计过程中出现的问题,把错误消灭在设计的初期,大大缩短开发周期,提高质量和效率。