生物信息数据库知识产权保护初探

生物信息技术是当今生命科学乃至整个自然科学的重大前沿领域之一,生物信息数据库是生物信息技术中非常重要的部分,对生命科学的发展起着重要的推动作用。本文叙述了生物信息数据库的特点及国内外知识产权保护现状,初步讨论了生物信息数据库知识产权保护中存在的问题,提出了保护我国生物信息数据库的建议。     

Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)

The 2010 International Conference on Bioinformatics, InCoB2010, which is the annual conference of the Asia-Pacific Bioinformatics Network (APBioNet) has agreed to publish conference papers in compliance with the proposed Minimum Information about a Bioinformatics investigation (MIABi), proposed in June 2009. Authors of the conference supplements in BMC Bioinformatics, BMC Genomics and Immunome Research have consented to cooperate in this process, which will include the procedures described herein, where appropriate, to ensure data and software persistence and perpetuity, database and resource re-instantiability and reproducibility of results, author and contributor identity disambiguation and MIABi-compliance. Wherever possible, datasets and databases will be submitted to depositories with standardized terminologies. As standards are evolving, this process is intended as a prelude to the 100 BioDatabases (BioDB100) initiative whereby APBioNet collaborators will contribute exemplar databases to demonstrate the feasibility of standards-compliance and participate in refining the process for peer-review of such publications and validation of scientific claims and standards compliance. This testbed represents another step in advancing standards-based processes in the bioinformatics community which is essential to the growing interoperability of biological data, information, knowledge and computational resources.     

A review of bioinformatics degrees in Australia

Bioinformatics has been a hot topic in Australia's biotechnology circles for the past five years. As with biotechnology in the 1990s, there has been a sudden increase in the number of Bioinformatics undergraduate degrees. For students in the 2005 intake there are six undergraduate Bioinformatics degrees to choose from and another five Bioinformatics streams within a Bachelor of Science degree. The courses vary from three to four years of full-time study. This report aims at dissecting each of these degrees to determine where the differences lie, to give the prospective students an idea as to which degree suits their career goals and to give an overview of the pedagogy of Australian bioinformatics education.     

数据挖掘在生物信息学中的应用

借助各种应用数学和计算机技术 ,将大量积累并急需处理的生物信息数据利用起来 ,探索生物信息中的规律 ,是当前国内国际生物信息学研究的热点和重点。其中数据挖掘技术在生物信息研究中发挥着巨大的作用。     

Bioinformatics and systems biology research update from the 15<Superscript>th</Superscript> International Conference on Bioinformatics (InCoB2016)

The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics and BMC Systems Biology, 24 articles with a bioinformatics or systems biology focus are reviewed in this editorial. InCoB2017 is scheduled to be held in Shenzen, China, September 20–22, 2017.     

Letter to the editor: Current progress in patient-specific modeling by Neal and Kerckhoffs (2010)

A recent review article on 'Current progress in patient-specific modeling' in Briefings in Bioinformatics contains the statement summarizing the results of our previous study 'On the unimportance of constitutive models in computing brain deformation for image-guided surgery' published in Biomechanics and Modeling in Mechanobiology as confirmation of adequacy of linear elastic model for such computation. The purpose of this Letter to the Editor is to clarify this statement by informing the Readers of Briefings in Bioinformatics that our study indicates the following: (i) a simple linear elastic constitutive model for the brain tissue is sufficient when used with an appropriate finite deformation solution (i.e. geometrically non-linear analysis); and (ii) Linear analysis approach that assumes infinitesimally small brain deformations leads to unrealistic results.     

MATLAB 7.X生物信息工具箱的应用--系统发生分析(五)

MATLAB 7.X生物信息工具箱为广大用户提供了一个用于系统发生分析的综合环境,它能利用数据库资源,方便获取DNA/蛋白质序列数据,所有操作简单高效,结果可视化程度高。在工具箱提供的开放环境里,用户还可以根据自己的目标来设计和利用分析工具。本文介绍MATLAB7.X生物信息工具箱在构建系统发生树方面的应用,以人科线粒体基因序列作为分子标记构建一株人科系统发生树为例,说明在MATLAB环境下对系统发生树的分析和处理。     

The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies

The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On January 9-11, 2006 the members as well as invited analysts came together at the European Bioinformatics Institute in Hinxton, UK for the pilot studies jamboree. The results of the reprocessing were presented and tasks forces were initiated to compile, to interpret and to summarise the data obtained.     

自然语言处理技术在生物信息学中的应用

从信息处理的角度来看,生物信息学与自然语言处理中的许多问题是非常相似的,因此,可以将一些自然语言处理中的经典方法应用到生物信息学文字中。本文介绍了自然语言处理和生物信息学中共有的问题,如比对、分类、预测等,以及这些问题的解决方法。通过对两个领域形似问题的分析可知,优秀的自然语言处理技术也可用来解决生物信息学方面的问题,并且一些还未在生物信息学领域得到应用的自然语言理解技术也有其潜在的应用价值。最后给出了一个分类问题的解决方案,演示了如何在生物数据上应用算法进行实验。     

Genes Selection Comparative Study in Microarray Data Analysis

In response to the rapid development of DNA Microarray Technologies, many differentially expressed genes selection algorithms have been developed, and different comparison studies of these algorithms have been done. However, it is not clear how these methods compare with each other, especially when we used different developments tools. Here, we considered three commonly used differentially expressed genes selection approaches, namely: Fold Change, T-test and SAM, using Bioinformatics Matlab Toolbox and R/BioConductor. We used two datasets, issued from the affymetrix technology, to present results of used methods and software''s in gene selection process. The results, in terms of sensitivity and specificity, indicate that the behavior of SAM is better compared to Fold Change and T-test using R/BioConductor. While, no practical differences were observed between the three gene selection methods when using Bioinformatics Matlab Toolbox. In face of our result, the ROC curve shows that: on the one hand R/BioConductor using SAM is favored for microarray selection compared to the other methods. And, on the other hand, results of the three studied gene selection methods using Bioinformatics Matlab Toolbox are still comparable for the two datasets used.     

MATLAB 7.X生物信息工具箱的应用——基因序列分析(一)

MATLAB 7.X生物信息工具箱为广大用户提供了一个用于基因组和蛋白质组分析的综合环境,它利用数据库资源,使科学研究事半功倍,在工具箱提供的开放环境里,用户甚至可以按照自己的目的来设计和利用分析工具.本文主要介绍了MATLAB7.X生物信息工具箱在基因序列分析中的应用,包括确定核苷酸组成,密码子组成,氨基酸转化和组成等,所有操作简便高效,结果可视化程度高.     

MATLAB7．X生物信息工具箱的应用——基因序列分析（一）

MATLAB7．X生物信息工具箱为广大用户提供了一个用于基因组和蛋白质组分析的综合环境,它利用数据库资源,使科学研究事半功倍,在工具箱提供的开放环境里,用户甚至可以按照自己的目的来设计和利用分析工具。本文主要介绍了MATLAB7．X生物信息工具箱在基因序列分析中的应用,包括确定核苷酸组成,密码子组成,氨基酸转化和组成等,所有操作简便高效。结果可视化程度高。     

基于电子克隆方法获得鸡MIBP全长cDNA

随着生物数据的急剧增长和计算机技术的快速提高,生物信息学这一新兴学科得到了前所未有的迅速发展,应用的领域越来越广。应用电子克隆技术来寻找未知新基因,就是生物信息学在全长新基因发现上的具体应用。电子克隆与其他发现全长基因的方法相比可以充分利用已有的数据库资源,避免大量的重复性劳动,节省时间和开支,加快新基因的发现。在鸡的大规模cDNA克隆测序的背景下,利用EST数据库比对,应用电子克隆技术来寻找鸡的末知新基因。并成功的预测了一个EST的全长cDNA序列物(947bp),同时对其进行了蛋白质水平的预测与分析,被步确定它编码206个氨基酸,其蛋白质序列与人肉整合素结合蛋白β1具有较高相似性(相似性为73%)。经RT-PCR扩增获得预期片断,测序鉴定,命名为ChickenMIBP。     

How to test bioinformatics software?

Biophysical Reviews - Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Bioinformatics programs developed for...     

Biggest challenges in bioinformatics

The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the ‘Biggest Challenges in Bioinformatics’ in a ‘World Café’ style event.     

生物信息学中的分布式计算

生物信息学的发展给计算机技术带来了挑战,通过介绍当前在生物信息学研究领域已经得到广泛使用或正在研发的各种分布式计算平台、工具或研究项目,以此来概观生物信息学领域中分布式计算应用的现状。     

生物信息学在发现新基因方面的应用

自生物信息学作为一门交叉学科诞生以来,其在计算机、农业和生命科学等各方面发挥了重要的作用,在后基因组时代,更是成为发现新基因的重要手段。对生物信息学的概况做了回顾与展望,并简述了生物信息学近年在发现新基因方面所取得的成果。     

The salmon genome (and other issues in bioinformatics)

A report on the fourth annual conference of the Society for Bioinformatics in the Nordic Countries (SOCBIN), Bioinformatics 2002, Bergen, Norway, 4-7 April 2002.     

SciRoKo: a new tool for whole genome microsatellite search and investigation

SciRoKo is a user-friendly software tool for the identification of microsatellites in genomic sequences. The combination of an extremely fast search algorithm with a built-in summary statistic tool makes SciRoKo an excellent tool for full genome analysis. Compared to other already existing tools, SciRoKo also allows the analysis of compound microsatellites. AVAILABILITY: free for use: www.kofler.or.at/Bioinformatics. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

MATLAB 7.X生物信息工具箱的应用———基因表达图谱分析（4）*

基因表达图谱原则上可了解整体细胞基因表达的信息,是基因组功能分析的重要研究手段。MATLAB 7.X生物信息工具箱为基因表达谱数据的分析和处理提供了一个综合环境,通过众多统计函数和绘图函数的结合使用,过滤不合格的基因数据和噪声数据,从而对基因表达数据进行聚类分析和主成分分析,绘制相关的基因表达图谱,完成基因芯片数据表达图谱的分析,分析结果可视化程度高,图表清晰、直观。本文主要以酿酒酵母Saccharomyces cerevisiae为例,详细描述了利用MATLAB 7.X生物信息工具箱对其基因表达图谱进行分析的过程。