Integration of a barcode reader with a commercial flow cytometer.

This report describes the application and installation of a barcode reader on a standard EPICS Elite flow cytometer. The barcode reader system eliminates keyboard entry of sample information on the cytometer. The system automates the transfer of sample information already present in our laboratory database to the cytometer at run time. The system uses a standard "off-the-shelf" bar code wand with a personal computer keyboard interface and requires no additional software at run time. No typing of sample information is required by the operator at any stage of normal sample operation at the cytometer. All operations are automatically coded into the cytometry software using the macro functions of the software. Tubes are inserted into the tube reader and sample information is transferred automatically into the cytometer. We have found that the system allows rapid and continuous operation of routine clinical and research samples. This automated data entry also reduces the possibility of data input errors.     

Development and Evaluation of Patient‐Centered Software for a Weight‐Management Clinic

Objective: To describe a weight‐management clinic software system and to report on its preliminary evaluation. Research Methods and Procedures: The software system standardizes the collection of relevant patient information from an initial medical assessment, weekly clinic visits, and laboratory testing protocol of a medically supervised proprietary meal‐replacement program in a university‐based referral clinic. It then generates monthly patient feedback reports with graphs of clinical and laboratory parameters to support a patient‐centered approach to weight management. After patients and clinic physicians review the data to ensure accuracy, the database is used for subsequent patient feedback reports, reports to referring physicians, quality assurance, and research. Clinic physicians and referring physicians were asked to rate their acceptance of the system. In addition, in a retrospective analysis of data generated by the system, outcomes for patients who received system‐generated feedback (n = 620) were compared with those who participated in the program before the introduction of feedback (n = 130). Results: Clinic and referring physicians reported that they had high overall satisfaction with the software and that the system saved them time, and the latter group reported that it decreased laboratory use. Regarding patients, the feedback group had lower dropout rates in the latter half of the program, better rates of attendance, completion of laboratory tests, and weight loss after 8 weeks. Discussion: The software seems to facilitate the effectiveness of the treatment protocol for obesity and generates a high‐quality database for patient care, clinic administration, quality assurance, and research purposes.     

CytoAccess, a relational laboratory information management system for a clinical cytogenetics laboratory

We developed a CytoAccess laboratory management system based on the widely used Microsoft Access software to facilitate data processing, result reporting, and quality management for a full-service cytogenetics laboratory. The CytoAccess system consists of four functional modules. The data entry module is for logging in patient information. The result entry module is used to generate chromosome, fluorescent in situ hybridization (FISH), and array comparative genomic hybridization (aCGH) reports. The administrative module enables periodic monitoring of quality control and quality improvement (QA/QI) parameters and produces billing forms. The maintenance module allows users to update clinical demographics, report templates, code tables, and to refresh data links. We have integrated into this system over 15,000 chromosome and FISH results from prenatal, postnatal, and cancer cases for the past six years. This system is cost-effective, user-friendly, flexible in updating, and potentially adaptable for data mining.     

A general signal-processing unit for electrophysiological measurements

A multipurpose electrophysiological signal-processing system using a small laboratory computer is presented as an essential tool for a new approach to medical instrumentation. The use of such a general measuring system for different diagnostic methods in the hospital instead of speial-purpose equipment for each method is elucidated, and hardware and software requirements of the system are defined. The hardware and software actually implemented in the system are described briefly, particular attention being paid to special software developments. Problems of software development and maintenance are discussed.     

Laboratory voice data entry system

We have assembled a system using a personal computer workstation equipped with standard office software, an audio system, speech recognition software and an inexpensive radio-based wireless microphone that permits laboratory workers to enter or modify data while performing other work. Speech recognition permits users to enter data while their hands are holding equipment or they are otherwise unable to operate a keyboard. The wireless microphone allows unencumbered movement around the laboratory without a "tether" that might interfere with equipment or experimental procedures. To evaluate the potential of voice data entry in a laboratory environment, we developed a prototype relational database that records the disposal of radionuclides and/or hazardous chemicals. Current regulations in our laboratory require that each such item being discarded must be inventoried and documents must be prepared that summarize the contents of each container used for disposal. Using voice commands, the user enters items into the database as each is discarded. Subsequently, the program prepares the required documentation.     

Intelligent software for laboratory automation

The automation of laboratory techniques has greatly increased the number of experiments that can be carried out in the chemical and biological sciences. Until recently, this automation has focused primarily on improving hardware. Here we argue that future advances will concentrate on intelligent software to integrate physical experimentation and results analysis with hypothesis formulation and experiment planning. To illustrate our thesis, we describe the 'Robot Scientist' - the first physically implemented example of such a closed loop system. In the Robot Scientist, experimentation is performed by a laboratory robot, hypotheses concerning the results are generated by machine learning and experiments are allocated and selected by a combination of techniques derived from artificial intelligence research. The performance of the Robot Scientist has been evaluated by a rediscovery task based on yeast functional genomics. The Robot Scientist is proof that the integration of programmable laboratory hardware and intelligent software can be used to develop increasingly automated laboratories.     

Error evaluation in the laboratory testing process and laboratory information systems

BackgroundThe laboratory testing process consist of five analysis phases featuring the total testing process framework. Activities in laboratory process, including those of testing are error-prone and affect the use of laboratory information systems. This study seeks to identify error factors related to system use and the first and last phases of the laboratory testing process using a proposed framework known as total testing process-laboratory information systems.MethodsWe conducted a qualitative case study evaluation in two private hospitals and a medical laboratory. We collected data using interviews, observations, and document analysis methods involving physicians, nurses, an information technology officer, and the laboratory staff. We employed the proposed framework and Lean problem solving tools namely Value Stream Mapping and A3 for data analysis.ResultsErrors in laboratory information systems and the laboratory testing process were attributed to failure to fulfill user requirements, poor cooperation between the information technology unit and laboratory, inconsistency of software design in system integration, errors during inter-system data transmission, and lack of motivation in system use. The error factors are related to system development elements, namely, latent failures that considerably affected the information quality and system use. Errors in system development were also attributed to poor service quality.ConclusionsComplex laboratory testing process and laboratory information systems require rigorous evaluation in minimizing errors and ensuring patient safety. The proposed framework and Lean approach are applicable for evaluating the laboratory testing process and laboratory information systems in a rigorous, comprehensive, and structured manner.     

Microcomputer control of behavior and the acquisition of digital and analog data

Advances in technology and decreasing costs are enabling microcomputers to displace more traditional devices in the scientific laboratory. The availability of various approaches to software-system development for the use of microcomputers in the on-line control of experiments has contributed to the trend. This report describes a software system developed to control conditioned behavior during schedules of reinforcement while simultaneously accumulating behavioral data and physiological (analog) data using a hardware system based on the Radio Shack TRS-80 Model I microcomputer. The software utilizes a high-level interpretive language (Microsoft BASIC), assembly language and compiled BASIC to attain an acceptable execution speed and ease of programming.     

SDAR: a practical tool for graphical analysis of two-dimensional data

ABSTRACT: BACKGROUND: Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionally, more complex software packages typically require more time by the individual user to understand and operate. Practical and convenient graphical data analysis software in Java with a user-friendly interface are rare. RESULTS: We have developed SDAR, a Java application to analyse two-dimensional data with an intuitive graphical user interface. A smart ASCII parser allows import of data into SDAR without particular format requirements. The centre piece of SDAR is the Java class GraphPanel which provides methods for generic tasks of data visualisation. Data can be manipulated and analysed with respect to the most common operations experienced in an experimental biochemical laboratory. Images of the data plots can be generated in SVG-, TIFF- or PNG-format. Data exported by SDAR is annotated with commands compatible with the Grace software. CONCLUSION: Since SDAR is implemented in Java, it is truly cross-platform compatible. The software is easy to install, and very convenient to use judging by experience in our own laboratories. It is freely available to academic users at http://www.structuralchemistry.org/pcsb/. To download SDAR, users will be asked for their name, institution and email address. A manual, as well as the source code of the GraphPanel class can also be downloaded from this site.     

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.     

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.     

“医学微生物学”本科实验教学中生物安全的落实与实践

"医学微生物学"实验课的主要实验材料是病原微生物,因此实验室生物安全是本课程区别于其它实验课程的重要特征之一。因条件限制,我校以前的"医学微生物学"实验课只能安排在不具备生物安全防护等级的普通实验室中进行,不仅存在安全隐患,也使一部分内容不能正常进行,使医学微生物实验教学的发展遇到了瓶颈。为解决这一矛盾,本研究通过医学微生物学教学师资队伍的培训、实验室硬件条件升级改造以及对课程内容涉及的菌(毒)种及其配套软件建设等一系列措施,建立了具有北京大学医学特色的"医学微生物学"实验教学新体系,保证了微生物实验室生物安全相关法规条例的落实及实验教学的正常进行。     

Automation of routine clinical chromosome analysis. I. Karyotyping by machine

An automated karyotyping system suitable for widespread use in clinical laboratories is described. The software is implemented on a general-purpose, commercially available image analyzer (Magiscan 2) using TV input from a conventional research microscope with minimal modification. The analysis is automatic, but operator interaction is used to resolve difficulties. Extensive experience with a routine clinical workload shows that the system is robust and easy to use and that its use results in a substantially increased laboratory throughput.     

Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group

A common challenge for bioinformaticians, in either academic or industry laboratory environments, is providing informatic solutions via the Internet or through a web browser. Recently, the open source community began developing tools for building and maintaining web applications for many disciplines. These content management systems (CMS) provide many of the basic needs of an informatics group, whether in a small company, a group within a larger organisation or an academic laboratory. These tools aid in managing software development, website development, document development, course development, datasets, collaborations and customers. Since many of these tools are extensible, they can be developed to support other research-specific activities, such as handling large biomedical datasets or deploying bioanalytic tools. In this review of open source website management tools, the basic features of content management systems are discussed along with commonly used open source software. Additionally, some examples of their use in biomedical research are given.     

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

Background  

New mathematical models of complex biological structures and computer simulation software allow modelers to simulate and analyze biochemical systems in silico and form mathematical predictions. Due to this potential predictive ability, the use of these models and software has the possibility to compliment laboratory investigations and help refine, or even develop, new hypotheses. However, the existing mathematical modeling techniques and simulation tools are often difficult to use by laboratory biologists without training in high-level mathematics, limiting their use to trained modelers.     

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.     

Integration of distributed multi-analyzer monitoring and control in bioprocessing based on a real-time expert system

A computer system solution for integration of a distributed bioreactor monitoring and control instrumentation on the laboratory scale is described. Bioreactors equipped with on-line analyzers for mass spectrometry, near-infrared spectroscopy, electrochemical probes and multi-array gas sensors and their respective software were networked through a real-time expert systems platform. The system allowed data transmission of more than 1800 different signals from the instrumentation, including signals from gas sensors, electrodes, spectrometer detectors, balances, flowmeters, etc., and were used for processing and carrying out a number of computational tasks such as partial least-square regression, principal component analysis, artificial neural network modelling, heuristic decision-making and adaptive control. The system was demonstrated on different cultivations/fermentations which illustrated sensor fusion control, multivariate statistical process monitoring, adaptive glucose control and adaptive multivariate control. The performance of these examples showed high operational stability and reliable function and meet typical requirements for production safety and quality.