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Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)最新文献

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Knowledge discovery in biological data sets using a hybrid Bayes classifier/evolutionary algorithm 基于混合贝叶斯分类器/进化算法的生物数据集知识发现
M. Raymer, L. Kuhn, W. Punch
A key element of bioinformatics research is the extraction of meaningful information from large experimental data sets. Various approaches, including statistical and graph theoretical methods, data mining, and computational pattern recognition, have been applied to this task with varying degrees of success. We have previously shown that a genetic algorithm coupled with a k-nearest-neighbors classifier performs well in extracting information about protein-water binding from X-ray crystallographic protein structure data. Using a novel classifier based on the Bayes discriminant function, we present a hybrid algorithm that employs feature selection and extraction to isolate salient features from large biological data sets. The effectiveness of this algorithm is demonstrated on various biological and medical data sets.
生物信息学研究的一个关键要素是从大型实验数据集中提取有意义的信息。各种方法,包括统计和图理论方法、数据挖掘和计算模式识别,已经应用于这项任务,并取得了不同程度的成功。我们之前已经证明,结合k近邻分类器的遗传算法在从x射线晶体学蛋白质结构数据中提取蛋白质-水结合信息方面表现良好。利用一种基于贝叶斯判别函数的分类器,我们提出了一种混合算法,该算法采用特征选择和提取来从大型生物数据集中分离显著特征。在各种生物和医学数据集上证明了该算法的有效性。
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引用次数: 11
Applying data warehouse concepts to gene expression data management 数据仓库概念在基因表达数据管理中的应用
V. Markowitz, T. Topaloglou
In this paper we present a method for applying data warehouse and on-line analytical processing concepts to gene expression data management. This method has been employed in developing the data management system that is used to host Gene Logic's GeneExpress(R) database products.
本文提出了一种将数据仓库和在线分析处理概念应用于基因表达数据管理的方法。该方法已应用于Gene Logic的GeneExpress(R)数据库产品的数据管理系统的开发。
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引用次数: 18
An automated approach to modelling class II MHC alleles and predicting peptide binding 建模II类MHC等位基因和预测肽结合的自动化方法
Martin T. Swain, A. J. Brooks, G. Kemp
We present an automated method for constructing 3D models of class II MHC structures that uses constraint logic programming to select side-chain conformations. The resulting models are used by a "peptide threading" program that attempts to predict peptides from a protein sequence that will bind strongly to particular MHC alleles. This method follows a comparative modelling approach in basing the model structures on experimentally determined MHC-peptide structures. However, constraints are used to ease open the peptide binding groove so that the modelled MHC structure is a less specific fit for the co-crystallised peptide in the starting structure. Preliminary results indicate that MHC models that have been constructed in this way enable the peptide threading program to make binding predictions that are comparable with those obtained when using experimentally determined MHC structures.
提出了一种利用约束逻辑编程选择侧链构象的自动构建II类MHC结构三维模型的方法。由此产生的模型被“肽线”程序所使用,该程序试图从一个蛋白质序列中预测肽,该蛋白质序列将与特定的MHC等位基因紧密结合。该方法采用比较建模方法,基于实验确定的mhc肽结构的模型结构。然而,限制条件被用来缓解打开肽结合槽,使模拟的MHC结构不太适合开始结构中的共结晶肽。初步结果表明,以这种方式构建的MHC模型使肽线程序能够做出与使用实验确定的MHC结构时获得的结果相当的结合预测。
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引用次数: 11
PocketMol: a molecular visualization tool for the Pocket PC PocketMol:用于Pocket PC的分子可视化工具
J. Gilder, M. Raymer, T. Doom
Molecular visualization programs are available on many platforms. They allow a user to visualize and manipulate molecular structures. PocketMol provides the same functionality on a Pocket PC handheld computer. Using standard protein data bank (pdb) files, the user can move, rotate, and scale a protein to explore its structure and function. The user can choose from a standard backbone view or a simplified view using only alpha carbon atoms. PocketMolGX uses the Microsoft Game API to provide fast animation that is quite smooth. PocketMol is designed as an aid for those wishing to explore or demonstrate protein structures without the availability of a full-size computer.
分子可视化程序可以在许多平台上使用。它们允许用户可视化和操纵分子结构。PocketMol在Pocket PC掌上电脑上提供相同的功能。使用标准的蛋白质数据库(pdb)文件,用户可以移动、旋转和缩放蛋白质以探索其结构和功能。用户可以选择标准的骨架视图或仅使用α碳原子的简化视图。PocketMolGX使用微软游戏API来提供非常流畅的快速动画。PocketMol是为那些希望在没有全尺寸计算机的情况下探索或演示蛋白质结构的人设计的辅助工具。
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引用次数: 3
Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs 通过最大化堆叠对的数量来预测具有任意假结的RNA二级结构
Samuel Ieong, M. Kao, T. Lam, W. Sung, S. Yiu
In this paper we investigate the computational problem of predicting RNA secondary structures that allow any kinds of pseudoknots. The general belief is that allowing pseudoknots makes the problem very difficult. Existing polynomial-time algorithms, which aim at structures that optimize some energy functions, can only handle a certain types of pseudoknots. In this paper we initiate the study of approximation algorithms for handling all kinds of pseudoknots. We focus on predicting RNA secondary structures with a maximum number of stacking pairs and obtain two approximation algorithms with worst-case approximation ratios of 1/2 and 1/3 for planar and general secondary structures, respectively. Furthermore, we prove that allowing pseudoknots would make the problem of maximizing the number of stacking pairs on planar secondary structure to be NP-hard. This result should be contrasted with the recent NP-hard results on psuedoknots which are based on optimizing some peculiar energy functions.
在本文中,我们研究了预测允许任何类型的假结的RNA二级结构的计算问题。一般的看法是允许假结使问题变得非常困难。现有的多项式时间算法,其目标是优化某些能量函数的结构,只能处理特定类型的伪结。本文研究了处理各种伪节的近似算法。我们着重于预测具有最大堆叠对数的RNA二级结构,并获得了平面和一般二级结构的两种最坏情况近似比分别为1/2和1/3的近似算法。此外,我们还证明了允许赝结的存在会使平面二级结构上的堆叠对数最大化问题变成NP-hard问题。这一结果应该与最近基于优化某些特殊能量函数的伪结的NP-hard结果进行对比。
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引用次数: 59
Supporting remote user defined functions in heterogeneous biological databases 支持异构生物数据库中远程用户定义的功能
Liangyou Chen, H. Jamil
Similar to most scientific studies, biological analyses demand a great deal of computations and simulations involving sophisticated tools that are often found geographically distributed over the Internet. A worldwide effort in genomics research has resulted in a powerful collection of publicly available sequence analysis tools. These tools often require specialized local services and domain knowledge to function correctly, rendering them unlikely candidates for integration into remote database applications. Thus, integration of heterogeneous "functions" still remains an open problem. Providing a reasonable framework for seamless integration of these tools with database query engines will enable application developers to exploit and harness the power of these effective analysis tools. In this paper, we present an integration framework for such tools by enabling access to them in a user transparent way as part of database queries. In our system, such online tools are abstracted as remote user defined functions (RUDF). An extended SQL DDL language, called the Internet Function Definition Language (IFDL), is presented for the specification and definition of RUDFs. The interface between database system and the Internet is implemented using a layer based on a language called the Hypertext Query Language (HTQL). The separation of IFDL, DDL, HTQL and SQL DML offers several optimization opportunities and makes it possible to develop an architecture for interoperability of heterogeneous databases with RUDFs in more simple and efficient ways.
与大多数科学研究类似,生物分析需要大量的计算和模拟,涉及复杂的工具,这些工具通常分布在互联网上。基因组学研究在全球范围内的努力已经导致了一个强大的收集公开可用的序列分析工具。这些工具通常需要专门的本地服务和领域知识才能正常工作,因此不太可能集成到远程数据库应用程序中。因此,异构“功能”的集成仍然是一个悬而未决的问题。为这些工具与数据库查询引擎的无缝集成提供一个合理的框架,将使应用程序开发人员能够利用和利用这些有效分析工具的强大功能。在本文中,我们为这些工具提供了一个集成框架,允许以用户透明的方式访问它们,作为数据库查询的一部分。在我们的系统中,这些在线工具被抽象为远程用户定义函数(RUDF)。提出了一种扩展的SQL DDL语言,称为Internet功能定义语言(IFDL),用于规范和定义rudf。数据库系统与Internet之间的接口使用一种基于超文本查询语言(Hypertext Query language, HTQL)的语言层来实现。IFDL、DDL、html和SQL DML的分离提供了一些优化机会,并使以更简单和有效的方式开发异构数据库与rudf互操作性的体系结构成为可能。
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引用次数: 9
Optimized seamless integration of biomolecular data 优化生物分子数据的无缝整合
B. Eckman, Z. Lacroix, L. Raschid
Today, scientific data is inevitably digitized, stored in a variety of heterogeneous formats, and is accessible over the Internet. Scientists need to access an integrated view of multiple remote or local heterogeneous data sources. They then integrate the results of complex queries and apply further analysis and visualization to support the task of scientific discovery. Building a digital library for scientific discovery requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web, as well as data that is locally materialized in warehouses or is generated by software. We consider several tasks to provide optimized and seamless integration of biomolecular data. Challenges to be addressed include capturing and representing source capabilities; developing a methodology to acquire and represent metadata about source contents and access costs; and decision support to select sources and capabilities using cost based and semantic knowledge, and generating low cost query evaluation plans.
今天,科学数据不可避免地被数字化,以各种异构格式存储,并可通过互联网访问。科学家需要访问多个远程或本地异构数据源的集成视图。然后,他们整合复杂查询的结果,并应用进一步的分析和可视化来支持科学发现的任务。建立一个用于科学发现的数字图书馆需要访问和操作从平面文件或数据库中提取的数据,从网络上检索的文档,以及在仓库中本地物化或由软件生成的数据。我们考虑了几个任务,以提供优化和无缝集成的生物分子数据。需要解决的挑战包括捕获和表示源能力;开发一种方法来获取和表示有关源内容和访问成本的元数据;以及使用基于成本和语义知识选择资源和功能的决策支持,并生成低成本的查询评估计划。
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引用次数: 45
An intelligent assistant for navigation of visually impaired people 为视障人士提供导航的智能助手
N. Bourbakis, D. Kavraki
This paper presents the navigation methodology employed by an intelligent assistant (agent) for people with disabilities. In particular, the intelligent assistant, called Tyflos, would help a visually impaired user to be partially independent and able to walk and work in a 3D dynamic environment. The Tyflos system carries two vision cameras and captures images from the surrounding 3D environment, either by the user's command or in a continuous mode (video), then it converts these images into verbal descriptions for each image into a verbal communication with the user. In other words the system plays the role of human assistant, who describes to the user the 3D visual environment.
本文介绍了一种用于残疾人的智能助手(agent)导航方法。特别值得一提的是,这款名为Tyflos的智能助手可以帮助视力受损的用户部分独立,并能够在3D动态环境中行走和工作。Tyflos系统携带两个视觉摄像头,通过用户的命令或连续模式(视频)从周围的3D环境中捕获图像,然后将这些图像转换为口头描述,每个图像转换为与用户的口头交流。换句话说,该系统扮演了人类助手的角色,向用户描述三维视觉环境。
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引用次数: 44
An XML application for genomic data interoperation 用于基因组数据互操作的XML应用程序
K. Cheung, Yang Liu, Anuj Kumar, M. Snyder, M. Gerstein, P. Miller
As the eXtensible Markup Language (XML) becomes a popular or standard language for exchanging data over the Internet/Web, there are a growing number of genome Web sites that make their data available in XML format. Publishing genomic data in XML format alone would not be that useful if there is a lack of development of software applications that could take advantage of the XML technology to process these XML-formatted data. This paper illustrates the usefulness of XML in representing and interoperating genomic data between two different data sources (Snyder's laboratory at Yale and SGD at Stanford). In particular, we compare the locations of transposon insertions in the yeast DNA sequences that have been identified by BLAST searches with the chromosomal locations of the yeast open reading frames (ORFs) stored in SGD. Such a comparison allows us to characterize the transposon insertions by indicating whether they fall into any ORFs (which may potentially encode proteins that possess essential biological functions). To implement this XML-based interoperation, we used NCBIs "blastall" (which gives an XML output option) and SGD's yeast nucleotide sequence dataset to establish a local blast server. Also, we converted the SGD's ORF location data file (which is available in tab-delimited formal) into an XML document based on the BIOML (BIOpolymer Markup Language) standard.
随着可扩展标记语言(eXtensible Markup Language, XML)成为在Internet/Web上交换数据的流行语言或标准语言,越来越多的基因组网站以XML格式提供数据。如果没有开发能够利用XML技术处理这些XML格式数据的软件应用程序,那么单独以XML格式发布基因组数据就没有多大用处。本文说明了XML在两个不同数据源(耶鲁大学Snyder的实验室和斯坦福大学SGD)之间表示和互操作基因组数据方面的有用性。特别地,我们将BLAST搜索确定的酵母DNA序列中的转座子插入位置与存储在SGD中的酵母开放阅读框(orf)的染色体位置进行了比较。这样的比较使我们能够通过指示转座子插入是否属于任何orf(可能编码具有基本生物学功能的蛋白质)来表征转座子插入。为了实现这种基于XML的互操作,我们使用ncbi的“blastall”(它提供了一个XML输出选项)和SGD的酵母核苷酸序列数据集来建立本地blast服务器。此外,我们还将SGD的ORF位置数据文件(以制表符分隔的形式提供)转换为基于BIOML(生物聚合物标记语言)标准的XML文档。
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引用次数: 2
Thinking nonlinearly about brain dynamics: a neurocommentary 关于大脑动力学的非线性思考:神经评论
Michale E. Brandt
Despite significant progress over the past several decades in neural research there still remains an ingrained tendency to approach the field using overly reductionistic as well as linear theories and methods. We are just beginning to appreciate the complexity of the brain. A further shift in our "consciousness" about neural dynamics is needed to take the next steps in brain research. We need to use more reflexively what we have learned about the nonlinear dynamical and complex nature of the brain to attempt to "bootstrap" our own thinking processes about neural science itself.
尽管在过去的几十年里,神经研究取得了重大进展,但仍然有一种根深蒂固的倾向,即使用过度还原论和线性理论和方法来接近该领域。我们才刚刚开始认识到大脑的复杂性。我们对神经动力学的“意识”需要进一步转变,才能在大脑研究中迈出下一步。我们需要更多地运用我们所学到的关于大脑的非线性动态和复杂本质的反射性知识,试图“引导”我们自己对神经科学本身的思考过程。
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引用次数: 3
期刊
Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)
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