生物实验信息管理模块建模技术研究

实验信息管理模块是生物实验室信息管理系统的核心,其设计的好坏直接关系到整个系统建设的成败。针对生物实验室实验流程灵活,数据流网络复杂等特点,研究设计了一套实验信息管理模块的模型,并将研究的模型用于基因测序实验室信息管理系统的开发并取得了成功。实践证明,该模型为实验室信息系统(LIMS)中实验管理模块的开发提供了理论支撑,并且提高了LIMS的开发效率。     

基于药物临床试验项目管理系统的临床试验全程管理

我国药物临床试验机构经过多年的发展,临床试验的试验条件质量有了一定的改善,但与发达国家相比,还存在着很多不足,应用信息化管理有助于提高药物临床试验质量管理。文章对医院II～IV期药物临床试验项目管理系统的总体功能进行介绍,该系统从临床试验项目管理出发,结合药物临床试验运行特点及流程,实现临床试验项目及药物全过程化管理,并与医院信息管理系统（HIS）、实验室信息管理系统（LIS）、医学影像信息系统（PACS）接口,构建起机构办、药物管理部门、检验检查科室与研究者之间的公共信息平台,实现了数据共享。     

提高医学实验室标本分析前质量控制方法的探讨

目的:探讨提高医学实验室标本分析前质量控制的方法。方法:根据《医学实验室质量和能力专用要求》(ISO15189)的分析前质量管理内涵并结合我院实验室实际情况,对流程再造前、后发生的总标本差错数进行对比分析。结果:通过完善实验室信息管理系统(LIS)的功能、实验室内部流程改造、对临床护士的培训等方面工作,流程再造前后有显著性差异(P<0.05)。结论:合理的分析前质量控制方法可提高医学实验室检测质量。     

灾难及突发事件住院信息管理系统的开发与实现

本文从系统设计目标、功能设计、结构设计等几个方面论述了灾难及突发事件住院信息管理系统的开发与实现。该系统由六大模块构成,实现了从预约管理、住院信息管理、床位管理、伤情评分、感染监测、查询统计到打印输出的灾害及突发时间住院伤病员信息全过程管理。应用本系统可规范灾害及突发事件医疗救援保障流程,大大提高了住院伤病员信息管理水平和工作效率。     

灾难及突发事件住院信息管理系统的开发与实现

本文从系统设计目标、功能设计、结构设计等几个方面论述了灾难及突发事件住院信息管理系统的开发与实现。该系统由六大模块构成,实现了从预约管理、住院信息管理、床位管理、伤情评分、感染监测、查询统计到打印输出的灾害及突发时间住院伤病员信息全过程管理。应用本系统可规范灾害及突发事件医疗救援保障流程,大大提高了住院伤病员信息管理水平和工作效率。     

基于C/S、B/S集成的高校科研型实验室综合信息管理系统的设计与实现

分析高校科学研究型实验室管理的现状,成功开发出基于C/S、B/S结合模式、集成多种实验室管理相关模块的新型实验室集成信息管理系统(Laboratory Information Management Systems,LIMS)。系统以实验室为核心、对人员、仪器、试剂耗材及整体环境进行全方位的综合管理。其应用及推广,对进一步提高科研型实验室管理水平,提高仪器使用效率,合理利用资源具有重要意义。可满足高校研究型实验室集成化信息管理的新需要。     

Windows操作系统下二代测序数据处理平台的建立及高通量信息分析标准流程在个人计算机上的实现

当前二代测序数据的处理广泛使用基于标准版本的Linux操作系统分析方法。这一系统专业性强,成本较高,操作界面不够友好,严重限制了大多数科研人员对数据的自主分析。本文创建了一个基于微软Windows操作系统的全功能二代测序数据的生物信息学分析系统,利用该系统经优选实现当前多种高通量测序数据的主流标准化分析流程。通过RNA-Seq的代表性案例,演算实测数据与传统Linux系统驱动的数据分析结果相比较,结果显示,本系统的组件和流程在常用的数据分析过程中,可以基本取代目前主流的Linux服务器或云计算平台,在运行效率相近的情况下,其操作极为简便且成本大大降低。本系统与所配附的编译软件及流程脚本,不仅为测序数据的生物信息学分析实操演练提供全面的解决方案,而且可以直接应用于专业的测序数据分析中。     

条形码自助取单系统的临床应用

目的：通过创建条形码自助取单系统,实现检验报告单发放的自动化、科学化和人性化管理,实现无纸化验室。方法：在检验信息管理系统与医院信息系统实现无缝连接的基础上,门诊患者在医生申请检验项目收费处确认收费后,由门诊抽血护士站采集标本时生成条形码和条形码取单凭证,患者用条形码取单凭证上的条形码在自动取单机上扫描打印所有检验报告单,住院患者由医生根据申请在医生工作站自行打印检验报告单。结果：条形码自助取单系统代替了传统人工分发检验报告单的繁琐、遗失和重复打印等问题,节省人力,使用方便。结论：利用条形码自助取单系统实现了检验报告单管理的自动化、规范化和实验室管理的科学化,杜绝了交叉污染,保护了病人隐私。     

古DNA单链测序文库的建立与检测北大核心CSCD

2005年问世的第二代测序技术在古DNA领域的应用,突破了第一代测序技术在绝灭或死亡生物全基因组获取手段上的局限。借助古基因组信息,研究者能够从更为系统的实时分子证据角度,解读诸如人类起源、大型绝灭哺乳动物迁移演化、动植物家养驯化以及早期人类社会生活模式等古生物学、遗传学与演化生物学问题。引入第二代测序技术之后,传统的古DNA研究方法及流程得以改变,剔除了原有的实验流程中耗时的分子克隆步骤,引入了与第二代测序技术紧密相关的古DNA单链测序文库构建环节。古DNA单链测序文库的构建,是将古DNA双链模板变性成单链后,通过向单链古DNA两端添加人工DNA片段,将古DNA分子转变成能被测序仪识别的文库分子。针对古DNA分子微量、高度片段化以及普遍存在碱基损伤的特点,古DNA单链测序文库,能够高效获取古DNA材料中的遗传信息。本文系统介绍古DNA单链测序文库建立流程,以及对文库质量进行检测的方法,为研究者运用第二代测序技术测定绝灭或死亡生物全基因组提供方法借鉴。     

ZZCDC数字化疾控信息管理系统的研究

ZZCDC 数字化疾控信息管理系统,采用 Web 的多层体系结构 Browse/Server 模式和 Oracle 中心数据库,将 CDC 工作流程进行功能化细分和模块化,构建成一个在线、实时、跨区域的互动式办公平台,涵盖了郑州市各级 CDC 的疾控信息管理、检验质控、存储归档、数据管理、信息共享等各方面业务,并通过 Internet 把各县区 CDC 疾控信息纳入网络管理,实现了郑州市疾控信息数据的操作交换和资源的共享．     

Integrating LIMS with MS Windows programs

PCs with MS-Office products (WORD, EXCEL) are commonly available at every workplace in analytical laboratories. These programs are used for data processing (EXCEL) and reporting (WORD). If a LIMS is available to store information the question often arises, if and how these WINDOWS programs can be integrated into a LIMS environment. The advantages are obvious: (a) the user can still employ his everyday programs; (b) a spreadsheet is often more appropriate for data input and processing than a LIMS; (c) automatic insertion of LIMS data into a Word document can simplify reporting considerably. Nevertheless, few points must be considered: (a) fast direct data access is necessary; (b) data validity must be guaranteed; (c) data are usually not transferred directly into the database but are presented to the LIMS as a file, which has to pass through a checking procedure; (d) GLP validation of all components (LIMS as well as EXCEL) is required. Our solutions. We employ SQL1LIMS from PE installed on an Alpha Vax under OpenVMS. For data input and reporting we developed several EXCEL spreadsheets. To extract data from the LIMS database we used the ODBC mechanism based on ORACLE SQL1NET 2. The ODBC connection is integrated into a visual-basic module of the EXCEL sheet. To ensure data validity we use the ‘LIST of Values’ method. A necessary prerequisite is a download from LIMS of a set of allowed values. Since with analytical data a check against a set of allowed values is often not possible, the amount of values necessary for checks is limited. Plausibility checks can well be performed within an EXCEL spreadsheet. To transfer data to LIMS we employ two mechanisms. A third (stored procedures) is being tested: (a) an NFS connection between a NOVELL-Netware Server and the LIMS—VAX; (b) ORACLE tables on the VAX, into which the data are loaded and then automatically spooled into the respective files. The NFS-connection between the Novell Server (Netware 4.1) and the VAX avoids the necessity for special drivers on the PC. This connection maps a VAX directory onto the PC.     

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/     

Recording information on protein complexes in an information management system

The Protein Information Management System (PiMS) is a laboratory information management system (LIMS) designed for use with the production of proteins in a research environment. The software is distributed under the CCP4 licence, and so is available free of charge to academic laboratories. Like most LIMS, the underlying PiMS data model originally had no support for protein-protein complexes. To support the SPINE2-Complexes project the developers have extended PiMS to meet these requirements. The modifications to PiMS, described here, include data model changes, additional protocols, some user interface changes and functionality to detect when an experiment may have formed a complex. Example data are shown for the production of a crystal of a protein complex. Integration with SPINE2-Complexes Target Tracker application is also described.     

A matrix for a LIMS with a strategic focus

This article focuses on the impact that a laboratory information management system (LIMS) should make on both a laboratory and an organisation but rarely does. To be effective a system should deliver benefit to both the laboratory environment and the organisation. But how should this be designed? To overcome this problem a matrix is proposed, which will allow any LIMS to be developed with a strategic focus. The matrix can be used either as an aid to system implementation and deciding which applications the LIMS should interface with. Alternatively, the matrix can be a means of evaluating the effectiveness of existing applications and to chart their further development. The aim is to give analytical chemists, managers and computer scientists a tool to enable any LIMS to reach its true potential.     

Integrating mass spectrometry data systems from different manufacturers in a local area network

Several scientific instruments suppliers are offering complete networking and automation packages for analytical laboratories. Nevertheless there is still considerable work to be done in the area of standardization of file formats generated by different data acquisition systems supplied by scientific instruments manufacturers. Recent work on the netCDF transfer protocol for mass spectrometry data suggests that good progress is being made in the area of data formats.Our laboratory operates a number of diverse instruments, including two high resolution systems (ZAB 2F, 70 SEQ) and one quadrupole (QMD 1000) from Fisons Instruments, one ion trap system from Finnigan (ITS 40) and one pyrolysis mass spectrometer from Horizon Instruments (RAPyD-400), all equipped with autosamplers. This instruments are physically located in two distinct laboratories. The data systems are based on very different computers, including a DEC PDP-11/24, a VAX 4000/90 and several PCs.The large amount of data produced by the MS laboratory and the implementation of GLPs, (Good Laboratory Practices) and GALPs (Good Automated Laboratory Practices) prompted us to examine the possibility of networking the instrumentation in a client/server computing environment. All instrument data systems have been connected to the institute network via ethernet, using either DECnet or TCP/IP. A VAXCluster consisting in a VAXStation 4000/90 host and a VAXStation 3100 satellite has been configured as a server using DEC PATHWORKS V.4.1 server software. This allows for file, disk, application and print services to all the PC clients connected network wide. Unattended distributed backup and restore services for PC hard disks are implemented. Mass spectrometry data files are permanently archived in their original format on 4 Gbyte tape cartridges and stored for later retrieval. Files can be transferred to any office PC running the appropriate mass spectrometry software. A centralized spectra and structure information management system based on the MassLib (Chemical Concepts) software allows for library searches using the SISCOM algorithm after specific file conversion programs or using JCAMP-DX files. Furthermore, the mass spectrometer data systems are readied for their eventual incorporation into a LIMS.     

SPINE 2: a system for collaborative structural proteomics within a federated database framework

We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium, allowing collaborative structural proteomics to be carried out in a distributed fashion. The core of SPINE is a laboratory information management system (LIMS) for key bits of information related to the progress of the consortium in cloning, expressing and purifying proteins and then solving their structures by NMR or X-ray crystallography. Originally, SPINE focused on tracking constructs, but, in its current form, it is able to track target sample tubes and store detailed sample histories. The core database comprises a set of standard relational tables and a data dictionary that form an initial ontology for proteomic properties and provide a framework for large-scale data mining. Moreover, SPINE sits at the center of a federation of interoperable information resources. These can be divided into (i) local resources closely coupled with SPINE that enable it to handle less standardized information (e.g. integrated mailing and publication lists), (ii) other information resources in the NESG consortium that are inter-linked with SPINE (e.g. crystallization LIMS local to particular laboratories) and (iii) international archival resources that SPINE links to and passes on information to (e.g. TargetDB at the PDB).     

构建基于磁珠微流控芯片的iFlora遗传信息高效获取系统

磁珠以其比表面积大、易与生物分子耦联、操控方便等优点,在生命科学中得到了广泛应用。随着微机电系统（MicroElectroMechanicalSystems,MEMS）技术的发展,将磁珠应用到微流控芯片中构建磁珠微流控分析系统,为生物样品分离、检测提供了一种全新方法。新一代植物志iFlora融入现代DNA测序技术．应用高速发展的信息、网络技术及云计算分析平台,收集、整合和管理植物物种相关信息,以实现物种智能鉴定和数据提取,而包括DNA条形码在内的遗传信息及其获取技术在iFlora中的作用至关重要。本文重点概述了基于纳米磁珠的微流控芯片技术及其在分子生物学领域中的应用,提出构建基于纳米磁珠微流控芯片的iFlora遗传信息采集系统,在微芯片上完成从DNA提取到测序全过程,实现物种遗传信息的快速、高效获取。     

WIST: toolkit for rapid, customized LIMS development

Workflow Information Storage Toolkit (WIST) is a set of application programming interfaces and web applications that allow for the rapid development of customized laboratory information management systems (LIMS). WIST provides common LIMS input components, and allows them to be arranged and configured using a flexible language that specifies each component's visual and semantic characteristics. WIST includes a complete set of web applications for adding, editing and viewing data, as well as a powerful setup tool that can build new LIMS modules by analyzing existing database schema. Availability and implementation: WIST is implemented in Perl and may be obtained from http://vimss.sf.net under the BSD license.     

LIMS — beyond CSV: a strategy for LIMS data quality assurance

Computer system validation of a LIMS is often confused with the ongoing task of entering and quality-assuring the material, instrument, specification, method, calculation, and study data required for laboratory sample and results management. A practical approach to LIMS template data quality assurance includes preparation of one or more standard operating procedures for entry and quality assurance of material specifications, test limits, secondary calculation formulae, and other analytical laboratory testing information.