基于网络的杂草标本管理信息系统的设计与开发

杂草标本在一定程度上反映了杂草物种的区域多样性及其分布 ,对于农田杂草的生物生态学研究、杂草的综合治理以及杂草资源的保护和持续利用都具有重要意义 ,是进行杂草科学研究的宝贵资源。在对全国杂草区系进行全面深入的调查、标本采集和鉴定工作的基础上 ,南京农业大学建立了中国杂草标本室 ,收藏的杂草标本涵盖全国 30个省、市、自治区 ,共有标本 3万余份 ,是我国目前数量最多、覆盖最广、包罗最完备的专业杂草标本室[1] 。国内外许多生物标本馆利用计算机数据库技术开发了标本管理信息系统[2 7] 。这些系统的开发 ,极大地方便了标本信…     

VSQual: a visual system to assist DNA sequencing quality control

A lack of pliant software tools that support small- to medium-scale DNA sequencing efforts is a major hindrance for recording and using laboratory workflow information to monitor the overall quality of data production. Here we describe VSQual, a set of Perl programs intended to provide simple and powerful tools to check several quality features of the sequencing data generated by automated DNA sequencing machines. The core program of VSQual is a flexible Perl-based pipeline, designed to be accessible and useful for both programmers and non-programmers. This pipeline directs the processing steps and can be easily customized for laboratory needs. Basically, the raw DNA sequencing trace files are processed by Phred and Cross_match, then the outputs are parsed, reformatted into Web-based graphical reports, and added to a Web site structure. The result is a set of real time sequencing reports easily accessible and understood by common laboratory people. These reports facilitate the monitoring of DNA sequencing as well as the management of laboratory workflow, significantly reducing operational costs and ensuring high quality and scientifically reliable results.     

A Laboratory Information Management System (LIMS) for a high throughput genetic platform aimed at candidate gene mutation screening

High throughput mutation screening in an automated environment generates large data sets that have to be organized and stored reliably. Complex multistep workflows require strict process management and careful data tracking. We have developed a Laboratory Information Management Systems (LIMS) tailored to high throughput candidate gene mutation scanning and resequencing that respects these requirements. Designed with a client/server architecture, our system is platform independent and based on open-source tools from the database to the web application development strategy. Flexible, expandable and secure, the LIMS, by communicating with most of the laboratory instruments and robots, tracks samples and laboratory information, capturing data at every step of our automated mutation screening workflow. An important feature of our LIMS is that it enables tracking of information through a laboratory workflow where the process at one step is contingent on results from a previous step. AVAILABILITY: Script for MySQL database table creation and source code of the whole JSP application are freely available on our website: http://www-gcs.iarc.fr/lims/. SUPPLEMENTARY INFORMATION: System server configuration, database structure and additional details on the LIMS and the mutation screening workflow are available on our website: http://www-gcs.iarc.fr/lims/     

Web-based weight management programs in an integrated health care setting: a randomized, controlled trial

Objective: To assess the efficacy of a Web‐based tailored behavioral weight management program compared with Web‐based information‐only weight management materials. Research Methods and Procedures: Participants, 2862 eligible overweight and obese (BMI = 27 to 40 kg/m²) members from four regions of Kaiser Permanente's integrated health care delivery system, were randomized to receive either a tailored expert system or information‐only Web‐based weight management materials. Weight change and program satisfaction were assessed by self‐report through an Internet‐based survey at 3‐ and 6‐month follow‐up periods. Results: Significantly greater weight loss at follow‐up was found among participants assigned to the tailored expert system than among those assigned to the information‐only condition. Subjects in the tailored expert system lost a mean of 3 ± 0.3% of their baseline weight, whereas subjects in the information‐only condition lost a mean of 1.2 ± 0.4% (p < 0.0004). Participants were also more likely to report that the tailored expert system was personally relevant, helpful, and easy to understand. Notably, 36% of enrollees were African‐American, with enrollment rates higher than the general proportion of African Americans in any of the study regions. Discussion: The results of this large, randomized control trial show the potential benefit of the Web‐based tailored expert system for weight management compared with a Web‐based information‐only weight management program.     

Infrastructures and services for remote sensing data production management across multiple satellite data centers

With the number of satellite sensors and date centers being increased continuously, it is becoming a trend to manage and process massive remote sensing data from multiple distributed sources. However, the combination of multiple satellite data centers for massive remote sensing (RS) data collaborative processing still faces many challenges. In order to reduce the huge amounts of data migration and improve the efficiency of multi-datacenter collaborative process, this paper presents the infrastructures and services of the data management as well as workflow management for massive remote sensing data production. A dynamic data scheduling strategy was employed to reduce the duplication of data request and data processing. And by combining the remote sensing spatial metadata repositories and Gfarm grid file system, the unified management of the raw data, intermediate products and final products were achieved in the co-processing. In addition, multi-level task order repositories and workflow templates were used to construct the production workflow automatically. With the help of specific heuristic scheduling rules, the production tasks were executed quickly. Ultimately, the Multi-datacenter Collaborative Process System (MDCPS) were implemented for large-scale remote sensing data production based on the effective management of data and workflow. As a consequence, the performance of MDCPS in experiments environment showed that those strategies could significantly enhance the efficiency of co-processing across multiple data centers.     

On Building Parallel &; Grid Applications: Component Technology and Distributed Services

Software Component Frameworks are well known in the commercial business application world and now this technology is being explored with great interest as a way to build large-scale scientific applications on parallel computers. In the case of Grid systems, the current architectural model is based on the emerging web services framework. In this paper we describe progress that has been made on the Common Component Architecture model (CCA) and discuss its success and limitations when applied to problems in Grid computing. Our primary conclusion is that a component model fits very well with a services-oriented Grid, but the model of composition must allow for a very dynamic (both in space and in time) control of composition. We note that this adds a new dimension to conventional service workflow and it extends the “Inversion of Control” aspects of most component systems. Dennis Gannon is a professor of Computer Science at Indiana University. He received his Ph.D. in Computer Science from the University of Illinois in 1980 and his Ph.D. in Mathematics from the University of California in 1974. From 1980 to 1985, he was on the faculty at Purdue University. His research interests include software tools for high performance distributed systems and problem solving environments for scientific computation. Sriram Krishnan received his Ph.D. in Computer Science from Indiana University in 2004. He is currently in the Grid Development Group at the San Diego Supercomputer Center where he is working on designing a Web services based architecture for biomedical applications that is secure and scalable, and is conducive to the creation of complex workflows. He received my undergraduate degree in Computer Engineering from the University of Mumbai, India. Liang Fang is a Ph.D. student in Computer Science at Indiana University. His research interests include Grid computing, Web services, portals, their security and scalability issues. He is a Research Assistant in Computer Science at Indiana University, currently responsible for investigating authorization and other security solutions to the project of Linked Environments for Atmospheric Discovery (LEAD). Gopi Kandaswamy is a Ph.D. student in the Computer Science Department at Indiana University where he is current a Research Assistant. His research interests include Web services and workflow systems for the Grid. Yogesh Simmhan received his B.E. degree in Computer Science from Madras University, India in 2000, and is a doctoral candidate in Computer Science at Indiana University. He is currently working as a Research Assistant at Indiana University, investigating data management issues in the LEAD project. His interests lie in data provenance for workflow systems and its use in data quality estimation. Aleksander Slominski is a Ph.D. student in the Computer Science at Indiana University. His research interests include Grid and Web Services, streaming XML Pull Parsing and performance, Grid security, asynchronous messaging, events, and notifications brokers, component technologies, and workflow composition. He is currently working as a Research Assistant investigating creation and execution of dynamic workflows using Grid Process Execution Language (GPEL) based on WS-BPEL.     

DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs

DataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow services. The use of an automated BioMoby workflow, rather than manual 'surfing', to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMoby Services enables fine-grained reusing of each service in other workflows, thus reducing the effort required to achieve similar investigations in the future. AVAILABILITY: The workflow is freely available as a Taverna SCUFL XML document at the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml.     

A workflow for mutation extraction and structure annotation

Rich information on point mutation studies is scattered across heterogeneous data sources. This paper presents an automated workflow for mining mutation annotations from full-text biomedical literature using natural language processing (NLP) techniques as well as for their subsequent reuse in protein structure annotation and visualization. This system, called mSTRAP (Mutation extraction and STRucture Annotation Pipeline), is designed for both information aggregation and subsequent brokerage of the mutation annotations. It facilitates the coordination of semantically related information from a series of text mining and sequence analysis steps into a formal OWL-DL ontology. The ontology is designed to support application-specific data management of sequence, structure, and literature annotations that are populated as instances of object and data type properties. mSTRAPviz is a subsystem that facilitates the brokerage of structure information and the associated mutations for visualization. For mutated sequences without any corresponding structure available in the Protein Data Bank (PDB), an automated pipeline for homology modeling is developed to generate the theoretical model. With mSTRAP, we demonstrate a workable system that can facilitate automation of the workflow for the retrieval, extraction, processing, and visualization of mutation annotations -- tasks which are well known to be tedious, time-consuming, complex, and error-prone. The ontology and visualization tool are available at (http://datam.i2r.a-star.edu.sg/mstrap).     

试析围手术期安全管理的切入点

通过建立信息技术控制体系和JCI标准下管理制度保障体系,不断优化工作流程,强化质量监控部门管理职能,定期开展临床技能培训,能够实现围手术期患者安全目标。     

上海农作物种质资源数据库的设计和构建

随着农作物种质资源数量的不断增加,种质资源交流的日益频繁以及种质资源利用的逐步深入,农作物种质资源数据库的建设对农作物的应用研究和基础性研究至关重要。上海市农业生物基因中心借助于本中心保存的近21万份种质资源的信息,开发了一套上海农作物种质资源数据库,本文主要阐述了该数据库设计和构建的目的、原则和数据库的架构、运行环境以及主要功能模块。上海农作物种质资源数据库采用了B/S结构,平台系统利用多层逻辑架构实现了对农作物种质资源数据信息的收集、存储、查询、统计分析等功能。外部用户通过浏览器即可访问平台系统,浏览查询种质资源信息。内部管理员可使用平台的受限功能,需要认证成功后才可使用后台管理功能,实现对整个平台数据的管理。注册用户还可通过基因资源数据库提交引种申请,管理员结合管理信息系统实现对外供种全流程的网络化,借此可提高工作效率,增加工作流程的透明度。     

Transparent mediation-based access to multiple yeast data sources using an ontology driven interface

Background

Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts.

Results

In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure.

Conclusions

Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis. The system can be accessed either through a cloud-enabled web-interface or downloaded and installed to run within the user's local environment. All resources related to Tavaxy are available at http://www.tavaxy.org.     

Performance metrics for evaluating system suitability in liquid chromatography—Mass spectrometry peptide mass mapping of protein therapeutics and monoclonal antibodies

The use of liquid chromatography – mass spectrometry (LC-MS) for the characterization of proteins can provide a plethora of information related to their structure, including amino acid sequence determination and analysis of posttranslational modifications. The variety of LC-MS based applications has led to the use of LC-MS characterization of therapeutic proteins and monoclonal antibodies as an integral part of the regulatory approval process. However, the improper use of an LC-MS system, related to intrinsic instrument limitations, improper tuning parameters, or poorly optimized methods may result in the production of low quality data. Improper system performance may arise from subtle changes in operating conditions that limit the ability to detect low abundance species. To address this issue, we systematically evaluated LC-MS/MS operating parameters to identify a set of metrics that can be used in a workflow to determine if a system is suitable for its intended purpose. Development of this workflow utilized a bovine serum albumin (BSA) digest standard spiked with synthetic peptides present at 0.1% to 100% of the BSA digest peptide concentration to simulate the detection of low abundance species using a traditional bottom-up workflow and data-dependent MS² acquisition. BSA sequence coverage, a commonly used indicator for instrument performance did not effectively identify settings that led to limited dynamic range or poorer absolute mass accuracy on 2 separate LC-MS systems. Additional metrics focusing on the detection limit and sensitivity for peptide identification were determined to be necessary to establish system suitability for protein therapeutic characterization by LC-MS.     

Topological analysis and interactive visualization of biological networks and protein structures

Computational analysis and interactive visualization of biological networks and protein structures are common tasks for gaining insight into biological processes. This protocol describes three workflows based on the NetworkAnalyzer and RINalyzer plug-ins for Cytoscape, a popular software platform for networks. NetworkAnalyzer has become a standard Cytoscape tool for comprehensive network topology analysis. In addition, RINalyzer provides methods for exploring residue interaction networks derived from protein structures. The first workflow uses NetworkAnalyzer to perform a topological analysis of biological networks. The second workflow applies RINalyzer to study protein structure and function and to compute network centrality measures. The third workflow combines NetworkAnalyzer and RINalyzer to compare residue networks. The full protocol can be completed in ～2 h.     

Performance metrics for evaluating system suitability in liquid chromatography—Mass spectrometry peptide mass mapping of protein therapeutics and monoclonal antibodies

The use of liquid chromatography – mass spectrometry (LC-MS) for the characterization of proteins can provide a plethora of information related to their structure, including amino acid sequence determination and analysis of posttranslational modifications. The variety of LC-MS based applications has led to the use of LC-MS characterization of therapeutic proteins and monoclonal antibodies as an integral part of the regulatory approval process. However, the improper use of an LC-MS system, related to intrinsic instrument limitations, improper tuning parameters, or poorly optimized methods may result in the production of low quality data. Improper system performance may arise from subtle changes in operating conditions that limit the ability to detect low abundance species. To address this issue, we systematically evaluated LC-MS/MS operating parameters to identify a set of metrics that can be used in a workflow to determine if a system is suitable for its intended purpose. Development of this workflow utilized a bovine serum albumin (BSA) digest standard spiked with synthetic peptides present at 0.1% to 100% of the BSA digest peptide concentration to simulate the detection of low abundance species using a traditional bottom-up workflow and data-dependent MS² acquisition. BSA sequence coverage, a commonly used indicator for instrument performance did not effectively identify settings that led to limited dynamic range or poorer absolute mass accuracy on 2 separate LC-MS systems. Additional metrics focusing on the detection limit and sensitivity for peptide identification were determined to be necessary to establish system suitability for protein therapeutic characterization by LC-MS.     

Web Proxy Acceleration

Numerous studies show that miss ratios at forward proxies are typically at least 40–50%. This paper proposes and evaluates a new approach for improving the throughput of Web proxy systems by reducing the overhead of handling cache misses. Namely, we propose to front-end a Web proxy with a high performance node that filters the requests, processing the misses and forwarding the hits and the new cacheable content to the proxy. Requests are filtered based on hints of the proxy cache content. This system, called Proxy Accelerator, achieves significantly better communications performance than a traditional proxy system. For instance, an accelerator can be built as an embedded system optimized for communication and HTTP processing, or as a kernel-mode HTTP server. Scalability with the Web proxy cluster size is achieved by using several accelerators. We use analytical models, trace-based simulations, and a real implementation to study the benefits and the implementation tradeoffs of this new approach. Our results show that a single proxy accelerator node in front of a 4-node Web proxy can improve the cost-performance ratio by about 40%. Hint-based request filter implementation choices that do not affect the overall hit ratio are available. An implementation of the hint management module integrated in Web proxy software is presented. Experimental evaluation of the implementation demonstrates that the associated overheads are very small.     

The Circulate architecture: avoiding workflow bottlenecks caused by centralised orchestration

As the number of services and the size of data involved in workflows increases, centralised orchestration techniques are reaching the limits of scalability. In the classic orchestration model, all data passes through a centralised engine, which results in unnecessary data transfer, wasted bandwidth and the engine to become a bottleneck to the execution of a workflow. This paper presents and evaluates the Circulate architecture which maintains the robustness and simplicity of centralised orchestration, but facilitates choreography by allowing services to exchange data directly with one another. Circulate could be realised within any existing workflow framework, in this paper, we focus on WS-Circulate, a Web services based implementation. Taking inspiration from the Montage workflow, a number of common workflow patterns (sequence, fan-in and fan-out), input to output data size relationships and network configurations are identified and evaluated. The performance analysis concludes that a substantial reduction in communication overhead results in a 2–4 fold performance benefit across all patterns. An end-to-end pattern through the Montage workflow results in an 8 fold performance benefit and demonstrates how the advantage of using the Circulate architecture increases as the complexity of a workflow grows.