Search

A system has been developed to electronically tag and track test tubes used in biorepositories. The system is based on a light-activated microtransponder, also known as a 'p-Chip.' One of the pressing problems with storing and retrieving biological samples at low temperatures is the difficulty of reliably reading the identification (ID) number that links each storage tube with the database containing sample details. Commonly used barcodes are not always reliable at low temperatures because of poor adhesion of the label to the test tube and problems with reading under conditions of frost and ice accumulation. Traditional radio frequency identification (RFID) tags are not cost effective and are too large for this application. The system described herein consists of the p-Chip, p-Chip-tagged test tubes, two ID readers (for single tubes or for racks of tubes), and software. We also describe a robot that is configured for retrofitting legacy test tubes in biorepositories with p-Chips while maintaining the temperature of the sample below −50°C at all times. The main benefits of the p-Chip over other RFID devices are its small size (600 × 600 × 100 μm) that allows even very small tubes or vials to be tagged, low cost due to the chip's unitary construction, durability, and the ability to read the ID through frost and ice. [ABSTRACT FROM AUTHOR]

Biorepositories in Africa need significant infrastructural support to meet International Society for Biological and Environmental Repositories (ISBER) Best Practices to support population-based genomics research. ISBER recommends a biorepository information management system which can manage workflows from biospecimen receipt to distribution. The H3Africa Initiative set out to develop regional African biorepositories where Uganda, Nigeria, and South Africa were successfully awarded grants to develop the state-of-the-art biorepositories. The biorepositories carried out an elaborate process to evaluate and choose a laboratory information management system (LIMS) with the aim of integrating the three geographically distinct sites. In this article, we review the processes, African experience, lessons learned, and make recommendations for choosing a biorepository LIMS in the African context. [ABSTRACT FROM AUTHOR]

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software () to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server-client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines. [ABSTRACT FROM AUTHOR]

Abstract: The Israel Police DNA database, also known as IPDIS (Israel Police DNA Index System), has been operating since February 2007. During that time more than 135,000 reference samples have been uploaded and more than 2000 hits reported. We have developed an effective semi-automated system that includes two automated punchers, three liquid handler robots and four genetic analyzers. An inhouse LIMS program enables full tracking of every sample through the entire process of registration, pre-PCR handling, analysis of profiles, uploading to the database, hit reports and ultimately storage. The LIMS is also responsible for the future tracking of samples and their profiles to be expunged from the database according to the Israeli DNA legislation. The database is administered by an in-house developed software program, where reference and evidentiary profiles are uploaded, stored, searched and matched. The DNA database has proven to be an effective investigative tool which has gained the confidence of the Israeli public and on which the Israel National Police force has grown to rely. [Copyright &y& Elsevier]

The rise of new experimental techniques, such as high-throughput combinatorial methods, and the availability of large data sets by means of the Internet have greatly increased the amount of data that must be managed by relatively small projects. Scientific data management systems developed for large projects are often not available, suitable, nor affordable for projects with lesser resources. Increasing numbers of open-source frameworks have made available numerous options for smaller facilities to build for themselves effective and robust data management solutions. We will present considerations of these options and a case study. [Copyright &y& Elsevier]

Abstract: The Emergency Response Management System is a customizable laboratory information management system (LIMS) developed to support chemical terrorism emergency response laboratory activities at the Centers for Disease Control and Prevention (CDC). Unique features of the LIMS include the following: (1) method profiles that provide an efficient tool for both validation and production experiments, (2) scalability of each assay to accommodate emergency surge-capacity needs, (3) standardized data formats for communicating between different instrument types and vendors, and (4) automated quality assurance communications that allow remote review and approval by CDC statisticians and supervisors. The system has been tested under exercise and real conditions for more than five years and has proved to be robust and effective. [Copyright &y& Elsevier]

Abstract: On January 1st, 2006, the Swedish legislation on obtaining DNA reference samples from suspects and the recording of DNA profiles in databases was changed. As a result the number of samples analysed at the Swedish National Laboratory of Forensic Science (SKL) increased from about 4500 in 2005 to more than 25,000 in 2006. To meet this challenge, SKL launched a new analysis system to create an unbroken chain, from sampling to incorporation of a profile in the national DNA database and subsequent automatic generation of digitally signed hit reports. The system integrates logistics, digital data transfer, new functions in LIMS (ForumDNA Version 4, Ida Infront AB) and laboratory automation. Buccal swab samples are secured on a FTA® card attached to an identity form, which is barcoded with a unique sample ID. After sampling, the police officer sends a digital request to SKL. The sample is automatically registered in LIMS and processed on delivery. The resulting DNA profiles are automatically classified according to quality using a custom-made expert system. Building the evaluation around mathematical rules makes it reproducible, standardised and minimises manual work and clerk errors. All samples are run in duplicate and the two profiles are compared within LIMS before incorporation in the database. In the first year of operation, the median time for completion of an analysis was 3 days, measured from delivery of the sample to incorporation of the profile in the national DNA database. In spite of the dramatic increase in the number of reference samples there was no backlog. [Copyright &y& Elsevier]

Sequencing of the human genome has opened the way and provided the impetus for building a comprehensive picture of a mammalian cell. Significant efforts are underway in the fields of genomics and proteomics to identify all genes and proteins in a given organism. The goal is a complete map of the genes, gene products, and their interaction networks in a functioning cell. The next step in establishing a comprehensive picture of a cell will be to integrate the cell''s metabolome with the rapidly developing genomic and proteomic maps. A cell''s metabolome, however, is such an enormous and complex entity that characterizing it can only be approached in sections. Our group of laboratories, the LIPID MAPS consortium, has focused on the lipid section of the metabolome. We have implemented a Lipid Metabolites and Pathways Strategy, termed LIPID MAPS, that applies a global integrated approach to the study of lipidomics in cells and tissues. This paper describes key aspects of the design, implementation, and accessibility features of a Laboratory Information Management System (LIMS) which serves the LIPID MAPS consortium. This software serves as a model system for integrating experimental information obtained by laboratories participating in metabolomics studies. [Copyright &y& Elsevier]

Serological surveillance testing for bovine brucellosis, Enzootic Bovine Leukosis, and Warble fly reaches approximately 1.7 million tests every year in the UK. An automated system was developed to improve the quality of data handling for all three surveys. The objectives were to make improvements in efficiency, sample tracking, and test reporting and to develop an epidemiological database. The developed system of bar-coded samples and test plates processed on automated equipment capable of scanning barcodes and transferring information across a computer network met the data objectives. Consolidating and automating the highly repetitive liquid-handling steps met the cost objectives. To reduce the impact of temporary bottlenecks in the system, a philosophy of ‘islands of automation’ was adopted to maximize the throughput. The creation of this system was driven largely by the need to have in place an effective emergency response capability to handle the serological needs of an outbreak of an acute and highly infectious veterinary disease such as Foot and Mouth Disease (FMD) in the UK. [Copyright &y& Elsevier]

An automated platform for low-volume, high-throughput protein crystallization by the sitting drop vapor diffusion has been developed. This platform consists of a novel Society of Biomolecular Screening standard microplate technology, standard automation liquid handling equipment, a software to design customizable, random crystallization buffers, an in-house designed scanner, a crystal recognition software, and Laboratory Information Management Systems. These technologies are designed to eliminate obstacles to the production of protein crystals and to address a number of critical issues faced by crystallography laboratories, namely precision and accuracy, ease of integration and use, speed, and cost. [Copyright &y& Elsevier]

Fully automating laboratory processes is a nontrivial task made more difficult by a lack of standardization between components. Each device in the system requires custom interfaces and translators to permit sharing of data and remote control by a central protocol. The BioCube System from Protedyne features the LILY data management software that enables communication between external databases, the robot controller, and integrated third-party devices. Data is formatted and passed internally as XML files to provide a generic interface for all the components. The resulting system allows the process to begin with the input of samples, and finish with the automatic export of data to a variety of data management software. [Copyright &y& Elsevier]

Single-nucleotide polymorphism (SNP) genotyping is a fundamental tool in the rapidly growing area of complex diseases and pharmacogenomics. SNP patterns that correlate with disease or response to treatment, respectively, are identified using bioinformatic techniques. We present an integrated laboratory information and management system (LIMS) for our high-throughput TaqMan™–based SNP genotyping platform. Three new client tools (ProjectManager, AssayManager, OrderTool) for our LIMS improve quality control and workflow management. The programs support organizing multiple genotyping experiments as projects, managing reagents with barcodes, and automation of assay ordering. The tools are freely available at our homepage. [Copyright &y& Elsevier]

Most of the scheduling software and instrument integration frameworks are written in Visual Basic, C/C++, or the LabView programming environment. A lot of these frameworks are proprietary tools of instrument vendors and are used by these companies during system integration of their instruments. In addition to the closed architecture of these products, the scheduler choice is very limited. ReTiSoft Inc. has created a suite of software products that address these problems. In this article we would like to introduce ReTiSoft''s open-architecture framework for instrument integration, a hybrid scheduler (static and dynamic) and a Web-enabled interface to the automated system. In addition to ReTiSoft''s integration framework (Genera) and the hybrid-scheduling software (Supra), we recently developed a Web-enabled application that allows scientists to log onto the automated system remotely, set up and run assays, examine and analyze the data produced during the experiment. The software is called DataPilot and is comprised of a high-performance database engine and the Apache Web server. In unison with Genera''s and Supra''s open-architecture approach, DataPilot can be modified and customized by system integrators to suit their specific application needs. The application serves as a data repository and adheres to guidelines presented by the Code of Federal Regulations for electronic records and electronic signatures; the guidelines are known as 21 CFR Part 11. This article provides an architectural overview of our software products and justifies its merits in comparison to other technologies commonly used in laboratories. We describe our Genera integration framework, give an overview of our scheduling algorithms, describe a Web-enabled data-tracking software and the enzyme-linked immunosorbent assay (ELISA assay), and describe different methods of automated system validation using our software. We also offer some conclusions. [Copyright &y& Elsevier]

This tutorial outlines some of the common risks that may be associated throughout the development and implementation of a laboratory automation project such as a laboratory information management system (LIMS) or another automation project. It presents a scheme for undertaking risk management to help assess and mitigate the degree of risk associated with each of these factors. In the case of high-risk factors, suggestions are presented to manage or help avoid the problem.Risk management is an ongoing process. It begins at the start of a project and should be reassessed at intervals throughout the project to re-evaluate existing risks and to see if any factors have changed or new ones have emerged. [Copyright &y& Elsevier]

At NFC the internally developed software for DNA analysis, SlimDna is used. It is complementary to the LIMS and keeps track of samples, sample batches, instrument files and generated data. The system communicates with the LIMS, instruments and other software. SlimDna includes four modules (Analysis, Control, Administration and Frequency calculation) and covers the entire analysis process from DNA extraction to reporting approved STR profiles to the LIMS. SlimDna is built with Microsoft Internet Information Services (IIS) as application server and the user interface consists of Windows clients. For data storage MySQL is used. The software has been implemented in different packages, STR typing being the latest. The system has streamlined the STR typing by providing, among other functions, automated evaluation of STR profiles, databases for observed variant alleles as well as tracking and logging of negative and positive controls. STR electropherograms from analysis of crime scene samples (around 30 000 per year) are evaluated by SlimDna according to set rules concerning for example stutter ratio, heterozygote balance and number of alleles per marker in order to define the profile as a single source genotype or a mixture. The SlimDna output is compared to a manual evaluation before the results are reported to the LIMS. This process saves nearly one minute hands-on time per sample compared to the previous Excel-based solution. For reference samples, SlimDna evaluates the majority (55%) of the samples without manual revision. SlimDna's automated interpretation has proven to be very accurate and will soon replace more of the manual revisions. In the near future, we aim to develop SlimDna further, with for example a mixture module supporting the reporting officers in analysis. [ABSTRACT FROM AUTHOR]

Abstract: The need for high-throughput laboratories to comply with regulatory requirements makes data management an important aspect of forensic genetics. A Laboratory Information Management System (LIMS) enables efficient workflows and ensures traceability if designed and implemented properly. We customized a commercial LIMS to support STR typing of reference samples according to in-house defined requirements. The customization focused on data validity, traceability and automated solutions. [Copyright &y& Elsevier]

Abstract: We have implemented and validated automated methods for washing FTA Card punches containing buccal samples and subsequent PCR setup using a Sias Xantus automated liquid handler. The automated methods were controlled by worklists generated by our LabWare Laboratory Information Management System (LIMS). The protocols were validated according to EN/ISO 17025 for use with STR amplifications kits AmpFℓSTR® Identifiler® and Y-filer® (Applied Biosystems). [Copyright &y& Elsevier]

Abstract: The new Swedish DNA legislation resulted in a huge increase in reference samples. In 2006 approximately 25,000 reference samples were received compared to 5000 in 2005. To meet this increase the reference samples had to be handled in a more automatic process than previously. A new module in the LIMS system automatically compares duplicate results and creates confirmed results if the DNA profiles meet the set requirements. Profiles without automatically confirmed results need to be manually investigated. Certain rules and settings in the LIMS sort these samples. Evaluators are able to combine the results to form confirmed results or chose to reanalyse the samples. At a rough estimate, 80% of all FTA samples are automatically assigned confirmed results, without any manual handling. Only 0.09% of the reference samples was terminated without results in every marker. [Copyright &y& Elsevier]

Abstract: IGNA is the first French laboratory for forensic DNA analysis. IGNA LIMS was developed from the software Microsoft Dynamics NAV which is an ERP (Enterprise Resource Planning) with a real opened solution for specific development and compatible with a lot of Microsoft applications. Thanks to the LIMS, we assure the traceability of analysis and also administrative process (traceability of letters, quotes or phone calls for each case and registration of actions to be done in a case (call for results …)). For one penal case, we can associate one or more sealed items. The DNA expert indicates the analysis to do on each piece (biological fluid detection, type of extraction, nuclear or mitochondrial DNA analysis …). During the technical process, samples automatically pass from a step to the next. Technicians indicate all the information needed for traceability (consumables lot number, used robots …). At the end of the process, the DNA expert validates his results, which are then directly transferred to the final report. Development of the IGNA LIMS from Microsoft Dynamics NAV allows us to use all specific applications of an ERP such as purchases, marketing, sales, etc. and to assure computerization of all our process, from quote to analysis report. [Copyright &y& Elsevier]