土壤食物网:结构、能流及稳定性

在国外4个土壤生态学项目的基础上,结合其他学者的研究成果,从连通网、能流网及功能网3个层次分别阐述了土壤食物网的结构、能流与稳定性。在连通网中,主要描述土壤食物网的功能群、营养位及格局;在能流网中,主要描述了面向过程食物网模型及其应用,主要涉及到土壤中的碳流与氮流;在功能网中,以作用强度为中心,描述了土壤食物网的稳定性问题。     

A web application to manage a database for liquid nitrogen tanks

Summary We have developed a software, Cell Database, for archiving records about cells stored in liquid nitrogen tanks. Once installed on a web server, the database is accessed through a standard web browser. This user-friendly and self-explanatory application is independent of computer platform and periodic upgrades of a commercial software. Our web application allows import of data from other database programs and adaptation to different tank formats, types of samples, and archiving needs.     

The Synergizer service for translating gene, protein and other biological identifiers

The Synergizer is a database and web service that provides translations of biological database identifiers. It is accessible both programmatically and interactively. AVAILABILITY: The Synergizer is freely available to all users inter-actively via a web application (http://llama.med.harvard.edu/synergizer/translate) and programmatically via a web service. Clients implementing the Synergizer application programming interface (API) are also freely available. Please visit http://llama.med.harvard.edu/synergizer/doc for details.     

Sigpep: calculating unique peptide signature transition sets in a complete proteome background

We have created a new software platform called sigpep that analyzes transition redundancy in selected reaction monitoring assays. Building on this platform, we also created a web application to generate transition sets with unique signatures for targeted peptides. The platform has been made available under the permissive Apache 2.0 open-source license, and the web application can be accessed from http://iomics.ugent.be/sigpep.     

Analysis and visualization of H7 influenza using genomic,evolutionary and geographic information in a modular web service

We have reported previously on use of a web‐based application, Supramap ( http://supramap.org ) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug‐resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY ( http://poyws.org ) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes ( http://geogenes.org ). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database. © The Willi Hennig Society 2012.     

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.     

A high performance integrated web data warehousing

Over the years, we have seen a significant number of integration techniques for data warehouses to support web integrated data. However, the existing works focus extensively on the design concept. In this paper, we focus on the performance of a web database application such as an integrated web data warehousing using a well-defined and uniform structure to deal with web information sources including semi-structured data such as XML data, and documents such as HTML in a web data warehouse system. By using a case study, our implementation of the prototype is a web manipulation concept for both incoming sources and result outputs. Thus, the system not only can be operated through the web, it can also handle the integration of web data sources and structured data sources. Our main contribution is the performance evaluation of an integrated web data warehouse application which includes two tasks. Task one is to perform a verification of the correctness of integrated data based on the result set that is retrieved from the web integrated data warehouse system using complex and OLAP queries. The result set is checked against the result set that is retrieved from the existing independent data source systems. Task two is to measure the performance of OLAP or complex query by investigating source operation functions used by these queries to retrieve the data. The information of source operation functions used by each query is obtained using the TKPROF utility.

Web portal to an image database for high-resolution three-dimensional reconstruction

The exponential increase of image data in high-resolution reconstructions by electron cryomicroscopy (cryoEM) has posed a need for efficient data management solutions in addition to powerful data processing procedures. Although relational databases and web portals are commonly used to manage sequences and structures in biological research, their application in cryoEM has been limited due to the complexity in accomplishing the dual tasks of interacting with proprietary software and simultaneously providing data access to users without database knowledge. Here, we report our results in developing web portal to SQL image databases used by the Image Management and Icosahedral Reconstruction System (IMIRS) to manage cryoEM images for subnanometer-resolution reconstructions. Fundamental issues related to the design and deployment of web portals to image databases are described. A web browser-based user interface was designed to accomplish data reporting and other database-related services, including user authentication, data entry, graph-based data mining, and various query and reporting tasks with interactive image manipulation capabilities. With an integrated web portal, IMIRS represents the first cryoEM application that incorporates both web-based data reporting tools and a complete set of data processing modules. Our examples should thus provide general guidelines applicable to other cryoEM technology development efforts.     

基于视联网的远程门诊系统应用探讨

远程门诊可拓展远程医疗服务范围和服务内容,将成为未来远程医疗发展的一种新型服务模式。文章介绍了远程门诊的概念和发展现状,分析了基于视联网技术的远程门诊系统框架和业务流程,探讨了基于视联网的远程门诊系统在远程门诊诊疗、门诊检查和门诊咨询等方面的应用及未来发展前景。     

The relative importance of the bacterial pathway and soil inorganic nitrogen increase across an extreme wood‐ash application gradient

Ash from combustion of biofuels, for example wood chips, is often deposited as waste, but due to its high content of essential plant nutrients and alkalinity, it has been proposed to recycle ash as a fertilizer and liming agent in biofuel production forest. However, current legislation sets rather strict limitations for wood‐ash application in biofuel production systems. The soil microfood web, that is microorganisms and their microfaunal grazers, protozoa and nematodes, is pivotal for essential ecosystem processes such as decomposition and plant nutrient release. Therefore, a thorough assessment of the impacts on microfood web structure and functioning must precede actions towards raising the currently allowed application rates. In a Danish Norway spruce plantation, we evaluate the impact of wood ash applied at dosages from 0 to the extreme case of 90 t ash ha^?1 on the microfood web, the bacterial community structure, soil content of inorganic nitrogen, organic matter, dissolved organic carbon and nitrogen. Using structural equation modelling (SEM), we disentangled the direct effect of the disturbance imposed by ash per se, the associated pH increase and changes in prey abundance on individual organism groups in the microfood web. The SEM showed that the pH rise was the main driver of increasing abundances of culturable heterotrophic bacteria with increasing ash doses, and via trophical transfer, this also manifested as higher abundances of bacterial grazers. Fungal‐feeding nematodes were unaffected by ash, whereas carnivorous/omnivorous nematodes decreased due to the direct effect of ash. Increasing ash doses enhanced the difference between bacterial communities of control plots and ash‐amended plots. The ash‐induced stimulation of culturable heterotrophic bacteria and bacterial grazers increased inorganic nitrogen availability at ash doses of 9 t ha^?1 and above. Hence, raised limits for ash application may potentially benefit tree growth via enhanced N mineralization activity of the soil food web.     

The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process

The Cell Cycle Ontology ( is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process. Cell Cycle Ontology is enabled by semantic web technologies, and is accessible via the web for browsing, visualizing, advanced querying, and computational reasoning. Cell Cycle Ontology facilitates a detailed analysis of cell cycle-related molecular network components. Through querying and automated reasoning, it may provide new hypotheses to help steer a systems biology approach to biological network building.     

Integration of gel-based proteome data with pProRep

pProRep is a web application integrating electrophoretic and mass spectral data from proteome analyses into a relational database. The graphical web-interface allows users to upload, analyse and share experimental proteome data. It offers researchers the possibility to query all previously analysed datasets and can visualize selected features, such as the presence of a certain set of ions in a peptide mass spectrum, on the level of the two-dimensional gel. AVAILABILITY: The pProRep package and instructions for its use can be downloaded from http://www.ptools.ua.ac.be/pProRep. The application requires a web server that runs PHP 5 (http://www.php.net) and MySQL. Some (non-essential) extensions need additional freely available libraries: details are described in the installation instructions.     

线虫区系分析指示土壤食物网结构和功能研究进展

土壤食物网结构复杂,功能众多,直接测定土壤食物网各功能群生物量并结合数学模型来推断土壤食物网结构和功能,工作量大且分析过程繁琐。线虫生态学的发展为土壤食物网的研究开辟了一条新的思路,即利用线虫区系分析来定性推断食物网的结构和功能。线虫作为土壤中数量最丰富的后生动物,占据着土壤食物网的中心位置,其物种多样性、食性多样性、生活史策略多样性、功能团多样性奠定了其作为土壤食物网结构和功能指示生物的生态学基础。线虫区系分析根据发展历史可以分为个体分类、生活史策略分类、功能团分类和代谢足迹分类四个时期,其中后两个时期主要用于推断土壤食物网结构和功能。基于功能团的线虫区系分析将线虫的食性和生活史策略结合起来,发展出一系列指数来判断土壤食物网的连通性、食物网链长度、外界养分投入情况、分解途径及对外界干扰的响应等。基于代谢足迹的线虫区系分析在功能团分析基础上,加入线虫能流分析,从而定性反映了土壤食物网功能的大小。两者在指示土壤食物网自下而上调节及对植物线虫控制等方面起着重要的作用。     

A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

Power management by load forecasting in web server clusters

The complexity and requirements of web applications are increasing in order to meet more sophisticated business models (web services and cloud computing, for instance). For this reason, characteristics such as performance, scalability and security are addressed in web server cluster design. Due to the rising energy costs and also to environmental concerns, energy consumption in this type of system has become a main issue. This paper shows energy consumption reduction techniques that use a load forecasting method, combined with DVFS (Dynamic Voltage and Frequency Scaling) and dynamic configuration techniques (turning servers on and off), in a soft real-time web server clustered environment. Our system promotes energy consumption reduction while maintaining user’s satisfaction with respect to request deadlines being met. The results obtained show that prediction capabilities increase the QoS (Quality of Service) of the system, while maintaining or improving the energy savings over state-of-the-art power management mechanisms. To validate this predictive policy, a web application running a real workload profile was deployed in an Apache server cluster testbed running Linux.     

ATV: display and manipulation of annotated phylogenetic trees

A Tree Viewer (ATV) is a Java tool for the display and manipulation of annotated phylogenetic trees. It can be utilized both as a standalone application and as an applet in a web browser.     

geoknife: reproducible web‐processing of large gridded datasets

Geoprocessing of large gridded data according to overlap with irregular landscape features is common to many large‐scale ecological analyses. The geoknife R package was created to facilitate reproducible analyses of gridded datasets found on the U.S. Geological Survey Geo Data Portal web application or elsewhere, using a web‐enabled workflow that eliminates the need to download and store large datasets that are reliably hosted on the Internet. The package provides access to several data subset and summarization algorithms that are available on remote web processing servers. Outputs from geoknife include spatial and temporal data subsets, spatially‐averaged time series values filtered by user‐specified areas of interest, and categorical coverage fractions for various land‐use types.     

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch.     

植保网络应用技术初步研究

ASP(Active Server Pages动态服务器网页）是Microsoft公司1997年推出的,WINDOWS面向WEB特征的,功能强大而成熟一种技术。2000年以来,笔对其应用于植保网络化、可视化与自动化方面作了一些探讨与开发,建立了我省第一个植保专业网站,网址www.fizb.com。阐述了植保在互联网上的初步应用研究。