Domino自动代理在移动办公中的应用

从移动办公的需求及特点出发,阐述了Lotus Notes中自动代理的优点.着重讲述了如何运用自动代理来实现Notes移动用户定期访问Domino服务器上的最近更新财务数据.将关系型数据库转换Notes文档数据库技术与Domino自动代理技术结合起来实现该功能,为解决OA开发相应的问题提供了一条可行的途径.     

一种基于图论的计算蛋白质数据库代表序列的算法

许多生物序列数据库中都含有大量的冗余序列,这些冗余序列通常不利于对数据库的统计分析和处理,而且它们要占用更多的计算机存储和处理资源.针对这个问题,本文中我们设计了一种去除蛋白质冗余序列的算法.该算法基于图论最大独立集的概念来生成非冗余序列集合,对目前存在的不少蛋白质去冗余程序所采用的由Hobohm和Sander最早设计的一种首先将序列分成若干簇然后取出代表序列的算法进行了改进,使得生成了更多的非冗余代表序列集合,避免了一些非冗余的序列也被去除.我们开发出了实现该算法的程序FastCluster,可以用来去除蛋白质数据库中的冗余序列.     

基于Java卡的移动代理系统安全模型

本文给出一个基于Java卡自行开发的移动代理系统JC-MAS，并从通信过程、主机执行环境和代理程序三方面研究系统安全策略，针对使用Java卡构建的JC-MAS安全模型设计了详细解决方案。     

中小企业的备份方案

信息系统的备份 Lotus Notes及Microsoft Exchange Server备份代理程序已经突破了技术上的限制,既可做在线即时备份,亦可仅针对已变动文档或部分资料夹进行备份及恢复。它们的做法是利用代理程序做为信息数据库及备份软件间的沟通桥梁,当启动备份操作时,备份软件就根据使用者设定的计划及工作描述,对备份代理程序送出系统要求,然后备份代理程序利用Notes及Exchange服务器的备份及恢复功能,从服务器中抓取数据库。接着备份代理程序会指示信息数据库,准备备份作业及数据库的数据,并送出要求的资料给备份软件,最后备份软件将资料写入使用者选择的目的磁盘装置。当备份作业完成时,备份代理程序会指示信息     

基于局域网的生物信息学应用与开发平台的建立

通过改写AceDB软件的部分源代码,扩展了AceDB数据库管理和图像显示的数据类型,并以自主开发的程序和免费软件Blast、wEMBOsS和AcePerl等建立了基于局域网的生物信息学应用与开发平台.初步建成的平台,集成了丰富的核酸与蛋白质序列分析工具及其他数据分析软件,与实验室各种生物学数据库连接整合,可进行深入的数据挖掘和知识发现.平台提供了多种语言的开发环境,可完成生物信息学新算法、新模型、新工具的设计与开发,开放的框架使平台具有良好的可扩展性及向后的兼容性.     

多代理数据库事务连接池的研究

为了解决数据库管理系统中事务请求拥塞问题,运用多代理技术设计了一种数据库事务连接池,该连接池具有良好的事务拥塞控制,事务自动拆解分配,异构数据库的识别等功能,使用多代理开发工具jade编写了相关代码。在连接控制技术和代理复用技术的比较实验中,验证了使用了代理复用技术的连接池更加稳定,具有优良的性能。最后利用多代理技术的灵活性实现了服务管理模块和事务分配模块用于解决连接池中复杂事务的处理问题。     

图符语言CQL解释器的实现

为了有效地实现数据库图符查询语言解释器,引入了图卡解析树;开发出二维文法规则;定义出一套适宜于模式分析、语法分析及语义解析的图符程序内部存储机制;并使用临时图卡的方法来解决带有嵌套结构的复杂语句的编译问题。     

基于Bioperl的生物二次数据库的设计与实现

在分子生物学研究中,建立二次数据库可以更深入的进行特色物种的研究。通过分析了构建生物信息二次数据库的复杂性和必要性,在MySQL数据库的基础上利用Bioperl相关技术提出了可行性方案,并给出了关键的构建步骤,最后建立了一个生物信息研究平台。     

基于Bioperl的生物二次数据库的设计与实现

在分子生物学研究中,建立二次数据库可以更深入的进行特色物种的研究。通过分析了构建生物信息二次数据库的复杂性和必要性,在MySQL数据库的基础上利用Bioperl相关技术提出了可行性方案,并给出了关键的构建步骤,最后建立了一个生物信息研究平台。     

Visual Basic.NET与数据库服务器连接方法改进

开发数据库应用系统,前台通常是用面向对象的开发语言,后台则需要用数据库软件来支持,如何简单、有效、智能的实现前台开发语言与后台数据库的连接,文章通过调用系统函数的方法实现了Visual Basic.NET与数据库服务器的自动连接,解决程序编码迁移后无法直接识别数据库服务器的问题。     

The GenBank nucleic acid sequence database

The GenBank nucleic acid sequence database is a computer-based collection of all published DNA and RNA sequences; it contains over five million bases in close to six thousand sequence entries drawn from four thousand five hundred published articles. Each sequence is accompanied by relevant biological annotation. The database is available either on magnetic tape, on floppy diskettes, on-line or in hardcopy form. We discuss the structure of the database, the extent of the data and the implications of the database for research on nucleic acids.     

ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage

ACNUC is a database structure and retrieval software for use with either the GenBank or EMBL nucleic acid sequence data collections. The nucleotide and textual data furnished by both collections are each restructured into a database that allows sequence retrieval on a multi-criterion basis. The main selection criteria are: species (or higher order taxon), keyword, reference, journal, author, and organelle; all logical combinations of these criteria can be used. Direct access to sequence regions that code for a specific product (protein, tRNA or rRNA) is provided. A versatile extraction procedure copies selected sequences, or fragments of them, from the database to user files suitable to be analysed by user-supplied application programs. A detailed help mechanism is provided to aid the user at any time during the retrieval session. All software has been written in FORTRAN 77 which guarantees a high degree of transportability to minicomputers or mainframes.     

Visualization of nucleic acid sequence structural information

Several interactive Pascal programs have been written for the analysis and display of structural information in nucleic acid sequences. Layout procedures were developed to display the homology and repeat matrices of a sequence and to predict and display the secondary structure of RNA/DNA molecules free of overlap and to predict and display internal repeats. No special plotting devices are required because the output is adapted to line printers. Sequences from several DNA database systems can be used as input. These programs are part of a general nucleic acid sequence analysis package.     

Compression of nucleic acid and protein sequence data

This paper describes the application of text compression methods to machine-readable files of nucleic acid and protein sequence data. Two main methods are used to reduce the storage requirements of such files, these being n-gram coding and run-length coding. A Pascal program combining both of these techniques resulted in a compression figure of 74.6% for the GenBank data-base and a program that used only n-gram coding gave a compression figure of 42.8% for the Protein Identification Resource database.     

A mechanism for maintaining an up-to-date GenBank database via Usenet

In this paper, we describe an automated system for distributing updates to the GenBank nucleic acid sequence database, using the Usenet news system as the underlying transport mechanism. Our system allows new loci to be distributed as soon as the sequences are available, over existing networks, using existing Usenet software and infrastructure currently available on a wide range of computer systems.     

Hypercard-based data management tools for molecular biologists.

I have designed a Macintosh data management system for molecular biologists. This system, called DataMinder, can be used to store information about oligonucleotides, nucleic acid or protein sequences, recombinant DNA clones, cells, reagents and protocols. DataMinder is not limited to data storage. A number of utilities for data analysis are provided, including those for the evaluation of oligonucleotides for use as hybridization probes or primers for DNA synthesis, and a variety of sequence editing features. Context-sensitive help is available on-line. DataMinder is simple to use and to customize and allows for sharing of database information across a computer network.     

Classification neural networks for rapid sequence annotation and automated database organization

A neural network classification method has been developed as an alternative approach to the search/organization problem of large molecular databases. Two artificial neural systems have been implemented on a Cray for rapid protein/nucleic acid classification of unknown sequences. The system employs a n-gram hashing function for sequence encoding and modular back-propagation networks for classification. The protein system, which classifies proteins into PIR (Protein Identification Resource) superfamilies, has achieved 82–100% sensitivity at a speed that is about an order of magnitude faster than other search methods. The pilot nucleic acid system showed a 91–97% classification accuracy. The software tool could be used as a filter program to reduce the database search time and help organize the molecular sequence databases. The tool is generally applicable to any databases that are organized according to family relationships.     

PRONUC: a software package for the analysis of protein and nucleic acid sequences

PRONUC is a menu-driven software package from which a molecular biologist may gain access to a variety of tools for the analysis of protein and nucleic acid sequences. Features include various algorithms for sequence comparisons, secondary structure prediction, sequence manipulation (translation complementation etc.) and finding restriction enzyme cut-sites. The sequences under study can be retrieved from several databases of published sequences or a users sequence(s) can be entered by means of a sequence editor or retrieved from a database constructed by the user. PRONUC comes with a comprehensive manual and on-line help which reflects several years of user feedback and is available for Digital VAX computer systems running the VMS or micro-VMS operating system.     

Easy to use and rapid isolation and detection of a viral nucleic acid by using paramagnetic microparticles and carbon nanotubes-based screen-printed electrodes

A method that is easy to use, rapid, with a low cost of detecting viral nucleic acid in a biological sample represents the essential tool in targeted therapy. In this study, we report the use of paramagnetic microparticles covered by streptavidin and modified by an oligonucleotide probe with a specific viral sequence labeled by biotin to detect human immunodeficiency virus (HIV) and influenza virus subtype H5N1. The viral nucleic acids were primarily detected by adsorptive transfer stripping technique coupled with square wave voltammetry using carbon paste, hanging mercury drop or carbon nanotubes-based screen-printed working electrodes. Detection limits were estimated for both sequences down to picograms per 3 μl. To isolate the viral sequences, paramagnetic microparticles covered with biotin-labeled oligonucleotides were used. We calculated the yield of isolation for H5N1 and/or HIV sequences, which was defined as “isolated concentration of viral nucleic acid sequence”/“given viral nucleic acid sequence” × 100. We estimated the yield for both sequences as 59%. Moreover, we studied the influence of human serum, dsDNA and non-complementary sequence of nucleic acids on isolation of viral nucleic acids. We also used carbon nanotubes-based screen-printed electrodes coupled with micro-flow instrument to detect viral nucleic acids. We were able to isolate and detect nanogram amounts of nucleic acids.