Cereal genome analysis using rice as a model

Researchers are eagerly waiting for the physical map of rice to become completed and available for use as a model for all cereals. The most significant advances of the past year have been the progress toward positional cloning of genes and the identification of quantitative trait loci (QTL) from detailed restriction fragment length polymorphism maps. Future focus will be: first, the enhanced dissemination and integration of the available data in World Wide Web accessible databases for easy comparison of genetic and physical mapping data across various species; second, the expanded distribution of a wide variety of DNA materials (cDNA clones, yeast artificial chromosomes, bacterial artificial chromosomes and other probes) for use in other cereals on the basis of the rice model map; and third, the applied breeding by locating and isolating sequences corresponding to important agronomic traits, often correlating with QTL.     

The aggregating behaviour of <Emphasis Type="Italic">Argiope radon</Emphasis>, with special reference to web decorations

The existence of aggregations in taxa that are normally solitary poses questions regarding the costs and benefits of group living. Most orb-web spiders are solitary and are aggressive to conspecifics, but a few species aggregate in large numbers. These spiders benefit by enhancing the prey interception potential, but also suffer costs of increased predation and parasitism. In this study, we report on the natural history characteristics of the orb-web spider, Argiope radon, which not only lives in aggregations but also builds silk decorations. Our results show that A. radon aggregates facultatively and that the main benefit of aggregation that we could identify is enhanced mating potential. We also show that decorations built by A. radon are highly visible to both model prey and predator, and suggest that solitary individuals with longer and more frequent decorations may offset the foraging advantage of being in aggregations.     

On-line self-checking of replication consistency for autonomic computing

In this paper we are concerned with the live verification of the consistency of a replicated system, an issue that has not been addressed by the research community so far. We consider the problem of how to enable the system to detect automatically and in production whether the invariants defining the correctness of object replication are violated. This feature could greatly improve the dependability of distributed applications and is necessary for constructing self-managing and self-healing replicated systems. We focus on systems that enforce strongly consistent replication: all replicas of each object must be kept “continuously” in-sync. This replication strategy is appropriate for application domains where correctness guarantees in spite of failures are more important than performance and scalability. We present the design and implementation of a replicated web service capable of self-checking whether all replicas are indeed kept in sync. This check occurs on-line, transparently to clients. We also discuss the performance cost of self-checking in our prototype. Alberto Bartoli is Associate Professor of Computer Engineering at the University of Trieste, Italy. He took a degree in Electrical Engineering in 1989 and a doctorate in Computer Engineering in 1994, both at the University of Pisa, Italy. His research interests are in the area of reliability and fault-tolerance in distributed systems. Giovanni Masarin took a degree in Electronic Engineering in 2004, at the University of Trieste, Italy. He is currently involved in product development at RadioTrevisan, a company specialized in the production of lawful interception equipments.     

基于CiteSpace的全球炭疽研究演化及其热点可视化分析

最新研究估算全球约有18.3亿人生活在炭疽风险区域内。经过几十年的发展,全球炭疽研究成果数量丰硕且总量在增长。【目的】对全球炭疽研究文献进行探析,以获取其研究领域演化趋势及热点变化。【方法】基于WOS来源文献,运用科学计量方法,对1998–2018年全球炭疽研究进行可视化分析,综合运用CiteSpace可视化分析软件中文献共被引、文献突现、关键词共现等工具,探析全球炭疽研究领域演化趋势及其热点变化。【结果】全球炭疽研究可分为1998–2004年"多维暴发"、2005–2013年"持续探索"和2014–2018年"新兴热点"3个研究阶段。【结论】炭疽快速实时痕量检测和新型炭疽疫苗有可能成为未来全球炭疽研究热点。     

关于秸秆微生物降解的文献计量分析

随着可再生生物质能源研究的快速发展,秸秆的微生物降解成为世界范围内的研究热点。客观分析当前秸秆微生物降解领域的发展态势,可为我国秸秆降解领域工作人员提供情报动态,推进我国在新型生物质能源方面的深入研究。本文基于WebofScience数据库,利用HisCite和VOSviewer软件分析工具,对世界范围内关于秸秆微生物降解领域的发文数量、高发文国家、高发文期刊及高发文机构等数据进行分析。分析结果发现秸秆微生物降解研究自21世纪以来出现逐年递增的趋势,全球范围内对秸秆微生物降解的研究主要集中在应用微生物、农业和生物技术等方面。其中,美国、中国、德国和日本在秸秆微生物降解研究领域处于国际领先地位。美国的发文量和发文的影响力位列首位。我国在该领域发文量位列第二名,表明我国在秸秆微生物降解领域的研究具有一定的基础,但影响力较低,需要加强高水平的研究,带动我国在该领域研究实力的整体提升。     

基于Web of Science的生物信息学文献分析

利用文献计量学方法,统计分析了1995—2007年11月Web of Science收录的生物信息学（bioinformatics）研究文献,探讨了生物信息学文献研究的年代分布、语种、期刊分布、作者、文献类型、主题分布以及发文量前10名的国家和机构,以期了解世界各国在这一研究领域的进展情况。     

马铃薯Y病毒属(Potyvirus)研究的文献计量分析

[目的]马铃薯Y病毒属(Potyvirus)是世界上最大的两个植物病毒属之一,对多种农作物造成危害.利用文献数据库,客观地分析国内外Potyvirus研究的发展动态,为国内外Potyvirus科研工作者和决策者提供参考.[方法]基于Web of Science数据库,采用文献计量学方法,对全球发表于1985-2012年的Potyvirus文献的国家、作者、机构、载文期刊及研究内容进行了数量和质量分析.[结果]检索到全球60个国家发表的Potyvirus文献2 442篇,以及每篇文献的被引频次和每个国家、机构及作者的H指数.经分析得出:全球Potyvirus研究论文的产出量自1991年呈稳定上升趋势,文献的数量和质量在统计的国家中,以美国最好,其次是法国、西班牙、澳大利亚、英国;美国的高产活跃作者最多;Potyvirus研究的热点是基因沉默和分子生物学,并随着研究技术方法的革新将不断深入;研究方向更多倾向于寄主方面的研究(如基因沉默、寄主抗性、与寄主互作等)及交叉学科;而中国在Potyvirus基础研究上距离国际先进水平还有很大距离,研究力量较少,有影响力的论文较少.[结论]美国在该领域的研究处于领先水平,我国仍需加强Potyvirus基础研究力量投入,努力缩短差距.     

MULTBLAST: A web application for multiple BLAST searches

Basic Local Alignment Search Tool, (BLAST) allows the comparison of a query sequence/s to a database of sequences and identifies those sequences that are similar to the query above a user-defined threshold. We have developed a user friendly web application, MULTBLAST that runs a series of BLAST searches on a user-supplied list of proteins against one or more target protein or nucleotide databases. The application pre-processes the data, launches each individual BLAST search on the University of Nevada, Reno''s-TimeLogic DeCypher® system (available from Active Motif, Inc.) and retrieves and combines all the results into a simple, easy to read output file. The output file presents the list of the query proteins, followed by the BLAST results for the matching sequences from each target database in consecutive columns. This format is especially useful for either comparing the results from the different target databases, or analyzing the results while keeping the identification of each target database separate.

Availability

The application is available at the URLhttp://blastpipe.biochem.unr.edu/     

Boca: an open-source RDF store for building Semantic Web applications

This article presents the design goals and features of the open-source Boca RDF server in the context of a community of cancer-tumor modeling investigators. Boca supplements the desirable data features of the Semantic Web with important enterprise and application features to power a new generation of Semantic-Web-based applications. The data features enable the integration and retrieval of tremendous quantities of diverse data. The enterprise features promote data integrity, fidelity, provenance and robustness. The application features provide for collaborative applications and dynamic user interfaces.     

Bringing Web 2.0 to bioinformatics

Enabling deft data integration from numerous, voluminous andheterogeneous data sources is a major bioinformatic challenge.Several approaches have been proposed to address this challenge,including data warehousing and federated databasing. Yet despitethe rise of these approaches, integration of data from multiplesources remains problematic and toilsome. These two approachesfollow a user-to-computer communication model for data exchange,and do not facilitate a broader concept of data sharing or collaborationamong users. In this report, we discuss the potential of Web2.0 technologies to transcend this model and enhance bioinformaticsresearch. We propose a Web 2.0-based Scientific Social Community(SSC) model for the implementation of these technologies. Byestablishing a social, collective and collaborative platformfor data creation, sharing and integration, we promote a webservices-based pipeline featuring web services for computer-to-computerdata exchange as users add value. This pipeline aims to simplifydata integration and creation, to realize automatic analysis,and to facilitate reuse and sharing of data. SSC can fostercollaboration and harness collective intelligence to createand discover new knowledge. In addition to its research potential,we also describe its potential role as an e-learning platformin education. We discuss lessons from information technology,predict the next generation of Web (Web 3.0), and describe itspotential impact on the future of bioinformatics studies.