我国生物信息产业的现状及问题分析

针对我国生物信息产业的现状及存在的问题进行分析,介绍了生物信息学以及生物芯片研究的现状和新技术、生物信息产业的发展,并对生物信息产业的知识产权保护问题进行了分析和讨论。对于今后如何发展我国生物信息产业以及如何采取策略和措施提供参考。     

生物信息学

生物信息学是采用计算机技术和信息论方法研究生命科学中各种生物信息的表达;采集,储存,传递,检索,分析和解读的科学,是现代生命科学与信息科学,计算机科学,数学,统计学,物理学,化学等学科相互渗透和高度交叉形成的学科,本文简要介绍了现代生物信息学的主要研究领域。     

充分利用Bioperl加速生物信息学的研究

Bioperl是Perl语言专门用于生物信息的工具与函数模块集,是世界各地的Perl开发人员在生物信息学、基因组学以及其他生命科学领域的智能结晶,服务于研究生物学问题的生物学家或计算机专家。通过对Bioperl进行了详细的介绍,并利用几个研究中的应用实例充分说明Bioperl在生物信息学研究中的重要地位。     

生物信息学数据库调查分析及其利用研究

从生物信息学数据库利用的角度调查分析生物信息学数据库的现状,为我国科研人员利用网上生物信息学数据库以及生物信息中心的开发提供科学依据和参考价值。研究采用网上调查的方法,对法国生物信息中心Infobiogen建立维护的生物信息学数据库目录DBcat中收录的511个数据库进行调查统计,分析其类型分布、国家分布、更新频率和获取方式;在此基础上。进一步利用欧洲分子生物学信息网(EMBnet)中30个成员国节点对生物信息学数据库利用现状进行统计分析。     

生物信息学在孤儿G蛋白偶联受体配基筛选中的应用

生物信息学的飞速发展为孤儿G蛋白偶联受体(orphan G protein—coupled receptors,oGPCRs)配基的筛选提供了重要的信息资源。利用生物信息学数据库和工具对oGPCRs的核酸和蛋白质序列进行运算、分析、注释和预测,获得足够的生物信息,辅助实验研究,以尽可能快速、准确地筛选出oGPCRs的特异性配基。本介绍有关生物信息学在oGPCRs配基筛选研究中的应用。     

主编寄语

近年来,在一批生物信息学先锋学者的大力推动下,随着国家层面支持力度的不断加大,我国生物信息学科已经有了长足的发展。为了科学、准确地报道我国生物信息理论与技术研发的重要成果和国内外生物信息技术及其产业化的最新进展,2003年经国家新闻出版     

农林院校生物信息学专业数据库技术课程教学改革刍议

生物信息学是一门交叉学科,对于现代生物学研究具有重要的意义。数据库技术是生物信息学的基础之一。本文对农林院校的生物信息学专业的数据库技术课程的教学现状做了一些介绍,对目前生物信息专业数据库教学存在的问题进行了分析。结合教学的实践,有针对性的提出了一些教学改革的具体措施。     

生物信息学在生物学研究领域的应用

综合叙述了生物信息学对生物学科研工作的影响,介绍了生物信息学在生物技术、生物医学、农业、食品、环境、能源等研究领域的应用概况,阐述了生物信息学为生物科研工作服务的意义。     

基于“天河二号”的水产病原生物信息分析平台构建及其在水产病原分析中的应用

作为生命科学的关键组成,生物信息学已被广泛地应用于基因组学、转录组学和蛋白质组学中。然而,生物信息分析平台的构建需要高性能计算机而非普通的个人电脑,从而极大地限制了生物信息学在水产科学中的应用。本研究基于“天河二号”超级计算机,构建了水产病原生物信息分析平台。该平台由基因组与转录组测序数据分析、蛋白质结构预测和分子动力学模拟3个功能模块组成。为了验证该平台的实用性,以水生动物病原微生物为例进行了生物信息学分析。通过Blast检索、GO和InterPro注释,鉴定了约氏黄杆菌(Flavobacterium johnsoniae)M168株的功能基因并对其进行了注释。通过同源模建,构建了草鱼呼肠孤病毒(Grass carp reovirus,GCRV)HZ-08的5个小节段的蛋白结构模型。对嗜水气单胞菌(Aeromonas hydrophila)外膜蛋白A进行了分子动力学模拟,并观察了平衡过程中系统温度、总能量、均方根偏差和环区构象的变化。以上结果均显示本研究成功建立了在“天河二号”超级计算机上运行的水产病原生物信息分析平台。此项研究将为其他学科生物信息分析平台的构建提供思路和线索。     

生物信息学本科专业建设现状

随着后基因组时代的到来,生物信息学逐渐进入了黄金发展期。生物信息学教育体系的建立和完善是永葆生物信息学活力的关键。国际和国内的生物信息学本科专业建设情况的分析显示全球生物信息学本科教育均处于起始阶段。深刻剖析了内蒙古自治区生物信息发展的瓶颈问题以及内蒙古科技大学开设生物信息学本科专业的优势和必要性。未来,随着测序技术、计算机技术等的进步,生物信息学将继续蓬勃发展;生物信息学人才的需求将不断扩大。为适应人才市场的需求,预计会有越来越多的高等院校将加入到中国的生物信息学本科教育事业。     

生物信息学在昆虫学研究中的应用

随着深度测序和基因芯片技术的不断发展,基因组、转录组、表达谱数据大量积累。目前,至少有10多个昆虫的基因组已被测序,30多个昆虫的转录组数据被报道。显然,传统的生物统计学方法无法处理如此海量的生物数据。量变引发质变,生物数据的大量积累催生了一门新兴学科,生物信息学。生物信息学融合了统计学、信息科学和生物学等各学科的理论和研究内容,在医学、基础生物学、农业科学以及昆虫学等方面获得了广泛的应用。生物信息学的目标是存储数据、管理数据和数据挖掘。因此,建立维护生物学数据库、设计开发基于模式识别、机器学习、数据挖掘等方法的生物软件,以及运用上述工具进行深度的数据挖掘,是生物信息学的重要研究内容。本文首先简要介绍了生物信息学的历史、研究现状及其在昆虫学科中的应用,然后综述了昆虫基因组学和转录组学的研究进展,最后对生物信息学在昆虫学研究中的应用前景进行了展望。     

后基因组时代的生物信息学

随着人类基因组计划的完成,不断积累的巨量的生物学数据和快速发展的信息学技术,给后基因组时代的生物信息学研究带来了新的挑战。该文对后基因组时代的生物信息学研究内容进行了比较全面的描述,分别就其研究对象和研究方向作了区别讨论,分析了生物信息学研究的现状和趋势,比较了国内外的研究发展情况和差距。针对我国在研究中所存在的主要问题,提出了建议并做了展望。     

Computational Biology and Bioinformatics in Nigeria

Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.     

Atlas – a data warehouse for integrative bioinformatics

Background  

We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development.     

Computer applications in biomolecular sciences. Part 2: bioinformatics and genome projects

This article defines and describes some of the basics of bioinformatics and projects aimed at sequencing entire genomes. Emphasis is placed on some of the ways in which the primary structures of nucleic acids and proteins may be investigated and analysed to gain meaningful biological information using computers and appropriate software. The importance of the world wide net and access to it is given prominence, particularly in bioinformatics research and teaching.     

A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer

Background  

In the study of cancer genomics, gene expression microarrays, which measure thousands of genes in a single assay, provide abundant information for the investigation of interesting genes or biological pathways. However, in order to analyze the large number of noisy measurements in microarrays, effective and efficient bioinformatics techniques are needed to identify the associations between genes and relevant phenotypes. Moreover, systematic tests are needed to validate the statistical and biological significance of those discoveries.     

A comparative study of cells in inflammation,EAE and MS using biomedical literature data mining

Summary Biomedical literature and database annotations, available in electronic forms, contain a vast amount of knowledge resulting from global research. Users, attempting to utilize the current state-of-the-art research results are frequently overwhelmed by the volume of such information, making it difficult and time-consuming to locate the relevant knowledge. Literature mining, data mining, and domain specific knowledge integration techniques can be effectively used to provide a user-centric view of the information in a real-world biological problem setting. Bioinformatics tools that are based on real-world problems can provide varying levels of information content, bridging the gap between biomedical and bioinformatics research. We have developed a user-centric bioinformatics research tool, called BioMap, that can provide a customized, adaptive view of the information and knowledge space. BioMap was validated by using inflammatory diseases as a problem domain to identify and elucidate the associations among cells and cellular components involved in multiple sclerosis (MS) and its animal model, experimental allergic encephalomyelitis (EAE). The BioMap system was able to demonstrate the associations between cells directly excavated from biomedical literature for inflammation, EAE and MS. These association graphs followed the scale-free network behavior (average γ = 2.1) that are commonly found in biological networks.     

Bioinformatic challenges for the next decade(s)

The science of bioinformatics has developed in the wake of methods to determine the sequences of the informational macromolecules--DNAs, RNAs and proteins. But in a wider sense, the biological world depends in its every process on the transmission of information, and hence bioinformatics is the fundamental core of biology. We here give a consideration of some of the key problems of bioinformatics in the coming decade, and perhaps longer.     

Bioinformatics in bioinorganic chemistry

Bioinformatics is a central discipline in modern life sciences aimed at describing the complex properties of living organisms starting from large-scale data sets of cellular constituents such as genes and proteins. In order for this wealth of information to provide useful biological knowledge, databases and software tools for data collection, analysis and interpretation need to be developed. In this paper, we review recent advances in the design and implementation of bioinformatics resources devoted to the study of metals in biological systems, a research field traditionally at the heart of bioinorganic chemistry. We show how metalloproteomes can be extracted from genome sequences, how structural properties can be related to function, how databases can be implemented, and how hints on interactions can be obtained from bioinformatics.