Laboratory Information Management System
Encyclopedia
Laboratory information system
A lab information system is a class of software that receives, processes, and stores information generated by medical laboratory processes. These systems often must interface with instruments and other information systems such as hospital information systems...
(LIS) or laboratory management system (LMS), a laboratory information management system (LIMS) is a software-based laboratory
Laboratory
A laboratory is a facility that provides controlled conditions in which scientific research, experiments, and measurement may be performed. The title of laboratory is also used for certain other facilities where the processes or equipment used are similar to those in scientific laboratories...
and information management system
System
System is a set of interacting or interdependent components forming an integrated whole....
that offers a set of key features that support a modern laboratory's operations. Those key features include — but are not limited to — workflow and data tracking support, flexible architecture, and smart data exchange interfaces, which fully "support its use in regulated environments." The features and uses of a LIMS have evolved over the years from simple sample tracking to an enterprise resource planning tool that manages multiple aspects of laboratory informatics
Laboratory informatics
Laboratory Informatics is the specialized application of information technology aimed at optimizing laboratory operations. It encompasses electronic lab notebooks, sample management, data acquisition, data processing, reporting and scientific data management...
.
Due to the rapid pace at which laboratories and their data management needs shift, the definition of LIMS has become somewhat controversial. As the needs of the modern laboratory vary widely from lab to lab, what is needed from a laboratory information management system also shifts. The end result is the definition of a LIMS is dependant upon the user. Dr. Alan McLelland of the Institute of Biochemistry, Royal Infirmary, Glasgow highlighted this problem in the late 1990s by explaining how a LIMS is perceived by an analyst, a laboratory manager, an information systems manager, and an accountant, "all of them correct, but each of them limited by the users' own perceptions."
Historically the LIMS, LIS, and process development execution system
Process Development Execution System
A Process Development Execution System is a system which is used by companies to perform development activities for high-tech manufacturing processes. A PDES is similar to a Manufacturing Execution Systems in several ways...
(PDES) have all performed similar functions. A LIMS has generally targeted environmental, research, or commercial analysis, such as pharmaceutical or petrochemical work, whereas the term "LIS" has tended to be used to reference lab informatics systems in the forensics and clinical markets, which often required special case management tools. The distinction between a LIS and LIMS has blurred in recent times, however, as most LIMS now fully support comprehensive case-centric data. The PDES normally addresses a wider scope, including, for example, virtual manufacturing techniques, while not necessarily integrating with laboratory equipment
Laboratory equipment
Laboratory equipment refers to the various tools and equipment used by scientists working in a laboratory. These include tools such as Bunsen burners, and microscopes as well as speciality equipment such as operant conditioning chambers, spectrophotometers and calorimeters...
.
More recently, LIMS products have been expanding even farther beyond their original purpose of sample management. Assay
Assay
An assay is a procedure in molecular biology for testing or measuring the activity of a drug or biochemical in an organism or organic sample. A quantitative assay may also measure the amount of a substance in a sample. Bioassays and immunoassays are among the many varieties of specialized...
data management, data mining
Data mining
Data mining , a relatively young and interdisciplinary field of computer science is the process of discovering new patterns from large data sets involving methods at the intersection of artificial intelligence, machine learning, statistics and database systems...
, data analysis, and electronic laboratory notebook
Electronic lab notebook
An electronic lab notebook is a software program designed to replace paper laboratory notebooks. Lab notebooks in general are used by scientists and technicians to document research, experiments and procedures performed in a laboratory...
(ELN) integration are all features that have been added to many LIMS, enabling the realization of translational medicine
Translational medicine
Translational medicine is a medical practice based on interventional epidemiology. It is regarded by its proponents as a natural progression from Evidence-Based Medicine. It integrates research from the basic sciences, social sciences and political sciences with the aim of optimising patient care...
completely within a single software solution.
History of LIMS
Up until the late 1970s, the management of laboratory samples and the associated analysis and reporting were time-consuming manual processes often riddled with transcription errors. This gave some organizations impetus to streamline the collection of data and how it was reported. Custom in-house solutions were developed by a few individual laboratories, while some enterprising entities at the same time sought to develop a more commercial reporting solution in the form of special instrument-based systems.In 1982 the first generation of LIMS was introduced in the form of a single centralized minicomputer, which offered laboratories the first opportunity to utilize automated reporting tools. As the interest in these early LIMS grew, industry leaders like Gerst Gibbon of the Federal Energy Technology Centre in Pittsburgh began planting the seeds of LIMS-related conferences. By 1988 the second-generation commercial offerings were tapping into relational database
Relational database
A relational database is a database that conforms to relational model theory. The software used in a relational database is called a relational database management system . Colloquial use of the term "relational database" may refer to the RDBMS software, or the relational database itself...
s to expand LIMS into more application-specific territory, and International LIMS Conferences were in full swing. As personal computer
Personal computer
A personal computer is any general-purpose computer whose size, capabilities, and original sales price make it useful for individuals, and which is intended to be operated directly by an end-user with no intervening computer operator...
s became more powerful and prominent, a third generation of LIMS emerged in the early 1990s. These new LIMS took advantage of the developing client/server architecture, allowing laboratories to implement better data processing and exchanges.
By 1995 the client/server tools had developed to the point of allowing processing of data anywhere on the network. Web-enabled LIMS were introduced the following year, enabling researchers to extend operations outside the confines of the laboratory. From 1996 to 2002 additional functionality was included in LIMS, from wireless network
Wireless network
Wireless network refers to any type of computer network that is not connected by cables of any kind. It is a method by which homes, telecommunications networks and enterprise installations avoid the costly process of introducing cables into a building, or as a connection between various equipment...
ing capabilities and georeferencing
Georeference
To georeference something means to define its existence in physical space. That is, establishing its location in terms of map projections or coordinate systems. The term is used both when establishing the relation between raster or vector images and coordinates, and when determining the spatial...
of samples, to the adoption of XML
XML
Extensible Markup Language is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications, all gratis open standards....
standards and the development of Internet purchasing.
Sample management
The core function of LIMS has traditionally been the management of samples. This typically is initiated when a sample is received in the laboratory, at which point the sample will be registered in the LIMS. This registration process may involve accessioning the sample and producing barcodeBarcode
A barcode is an optical machine-readable representation of data, which shows data about the object to which it attaches. Originally barcodes represented data by varying the widths and spacings of parallel lines, and may be referred to as linear or 1 dimensional . Later they evolved into rectangles,...
s to affix to the sample container. Various other parameters such as clinical or phenotypic
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
information corresponding with the sample are also often recorded. The LIMS then tracks chain of custody as well as sample location. Location tracking usually involves assigning the sample to a particular freezer location, often down to the granular level of shelf, rack, box, row, and column. Other event tracking such as freeze and thaw cycles that a sample undergoes in the laboratory may be required.
Modern LIMS have implemented extensive configurability as each laboratory's needs for tracking additional data points can vary widely. LIMS vendors cannot typically make assumptions about what these data tracking needs are, and therefore vendors must create LIMS that are adaptable to individual environments. LIMS users may also have regulatory concerns to comply with such as CLIA, HIPAA, GLP
GLP
GLP can refer to:* Gateway location protocol* German Longhaired Pointer* Gibraltar Labour Party* Gibraltar Liberal Party* Gleichmäßigkeitsprüfung, German for regularity test, a series for street-legal cars held at Nürburgring* Global Land Project...
, and FDA specifications, affecting certain aspects of sample management in a LIMS solution. One key to compliance with many of these standards is audit logging of all changes to LIMS data, and in some cases a full electronic signature
Electronic signature
An electronic signature, or e-signature, is any electronic means that indicates either that a person adopts the contents of an electronic message, or more broadly that the person who claims to have written a message is the one who wrote it . By comparison, a signature is a stylized script...
system is required for rigorous tracking of field-level changes to LIMS data.
Instrument and application integration
Modern LIMS offer an increasing amount of integration with laboratory instruments and applications. A LIMS may create control files that are "fed" into the instrument and direct its operation on some physical item such as a sample tube or sample plate. The LIMS may then import instrument results files to extract data for quality control assessment of the operation on the sample. Access to the instrument data can sometimes be regulated based on chain of custody assignments or other security features if need be.A relatively new development in LIMS products is the ability to import and manage raw assay
Assay
An assay is a procedure in molecular biology for testing or measuring the activity of a drug or biochemical in an organism or organic sample. A quantitative assay may also measure the amount of a substance in a sample. Bioassays and immunoassays are among the many varieties of specialized...
data results. Modern targeted assays such as qPCR and deep sequencing can produce tens of thousands of data points per sample. Furthermore, in the case of drug and diagnostic development as many as 12 or more assays may be run for each sample. In order to track this data, a LIMS solution needs to be adaptable to many different assay formats at both the data layer and import creation layer, while maintaining a high level of overall performance. Some LIMS products address this by simply attaching assay data as BLOB
Binary large object
A blob is a collection of binary data stored as a single entity in a database management system. Blobs are typically images, audio or other multimedia objects, though sometimes binary executable code is stored as a blob...
s to samples, but this limits the utility of that data in data mining and downstream analysis.
Electronic data exchange
The exponentially growing volume of data created in laboratories coupled with increased business demands and focus on profitability have pushed LIMS vendors to increase attention to how their LIMS handles electronic data exchangesElectronic Data Interchange
Electronic data interchange is the structured transmission of data between organizations by electronic means. It is used to transfer electronic documents or business data from one computer system to another computer system, i.e...
. Attention must be paid to how an instrument's input and output data is managed, how remote
sample collection data is imported and exported, and how PDAs and tablet technology integrates with the LIMS. The successful transfer of data files in Microsoft Excel and other formats, as well as the import and export of data to Oracle, SQL, and Microsoft Access databases is a pivotal aspect of a the modern LIMS. In fact, the transition "from proprietary databases to standardized database management systems such as Oracle ... and SQL" has arguably had one of the biggest impacts on how data is managed and exchanged in laboratories.
Additional functions
Aside from the key functions of sample management, instrument and application integration, and electronic data exchange, there are numerous additional operations that can be managed in a LIMS. This includes but is not limited to:audit
Audit
The general definition of an audit is an evaluation of a person, organization, system, process, enterprise, project or product. The term most commonly refers to audits in accounting, but similar concepts also exist in project management, quality management, and energy conservation.- Accounting...
management
- fully track and maintain an audit trail
barcode
Barcode
A barcode is an optical machine-readable representation of data, which shows data about the object to which it attaches. Originally barcodes represented data by varying the widths and spacings of parallel lines, and may be referred to as linear or 1 dimensional . Later they evolved into rectangles,...
handling
- assign one or more data points to a barcode format; read and extract information from a barcode
chain of custody
- assign roles and groups that dictate access to specific data records and who is managing them
compliance
- follow regulatory standards that affect the laboratory
customer relationship management
- handle the demographic information and communications for associated clients
document management
- process and convert data to certain formats; manage how documents are distributed and accessed
instrument calibration
Calibration
Calibration is a comparison between measurements – one of known magnitude or correctness made or set with one device and another measurement made in as similar a way as possible with a second device....
and maintenance
- schedule important maintenance and calibration of lab instruments and keep detailed records of such activities
inventory and equipment management
- measure and record inventories of vital supplies and laboratory equipment
manual and electronic data entry
- provide fast and reliable interfaces for data to be entered by a human or electronic component
method management
- provide one location for all laboratory process and procedure (P&P) and methodology to be housed and managed
personnel and workload management
- organize work schedules, workload assignments, employee demographic information, and financial information
quality assurance and control
- gauge and control sample quality, data entry standards, and workflowWorkflowA workflow consists of a sequence of connected steps. It is a depiction of a sequence of operations, declared as work of a person, a group of persons, an organization of staff, or one or more simple or complex mechanisms. Workflow may be seen as any abstraction of real work...
reports
- create and schedule reports in a specific format; schedule and distribute reports to designated parties
time tracking
- calculate and maintain processing and handling times on chemical reactions, workflows, and more
Client-side LIMS options
A LIMS can use many delivery technologies. Thin-client LIMS implementations — including Java-based solutions — often require no special client-sideClient-side
Client-side refers to operations that are performed by the client in a client–server relationship in a computer network.Typically, a client is a computer application, such as a web browser, that runs on a user's local computer or workstation and connects to a server as necessary...
installation resulting in less IT involvement in their deployment. An exception is a web-based solution based on .NET
.NET Framework
The .NET Framework is a software framework that runs primarily on Microsoft Windows. It includes a large library and supports several programming languages which allows language interoperability...
technologies, requiring a special plug-in on the client and may be limited to Microsoft only browsers. This can lead to issues in instances where there is a high penetration of Apple and Linux usage by lab technicians or researchers. Another concern regarding web-based and web-enabled deployment is possible exploitation by hackers where highly sensitive laboratory and research data may be compromised. Even with modern security methods in place, deploying a LIMS solution "outside the firewall" of an organization opens the LIMS to potential intrusion.
The following represent the four most-used LIMS architectures, and their associated strengths and weaknesses:
Thick-client
A thick-client LIMS is a more traditional client/server architecture, with some of the system residing on the computer or workstation of the user (the client) and the rest on the server. The LIMS software is installed on the client computer, which does all of the data processing. Later it passes information to the server, which has the primary purpose of data storage. Most changes, upgrades, and other modifications will happen on the client side. This was one of the first architectures implemented into a LIMS, having the advantage of providing higher processing speeds (because processing is done on the client and not the server) and slightly more security (as access to the server data is limited only to those with client software). Additionally, thick-client systems have the added advantage of providing more interactivity and customization, though often at a greater learning curve. The disadvantages of client-side LIMS include the need for more robust client computers and more time-consuming upgrades, as well as a lack of base functionality through a web browserWeb browser
A web browser is a software application for retrieving, presenting, and traversing information resources on the World Wide Web. An information resource is identified by a Uniform Resource Identifier and may be a web page, image, video, or other piece of content...
. The thick-client LIMS can become web-enabled through an add-on component.
Thin-client
A thin-client LIMS is a more modern architecture which offers full application functionality accessed through a device's web browser. The actual LIMS software resides on a server (host) which feeds and processes information without saving it to the user's hard disk. Any necessary changes, upgrades, and other modifications are handled by the entity hosting the server-side LIMS software, meaning all end-users see all changes made. To this end, a true thin-client LIMS will leave no "footprint" on the client's computer, and only the integrity of the web browser need be maintained by the user. The advantages of this system include significantly lower cost of ownership and fewer network and client-side maintenance expenses. However, this architecture has the disadvantage of requiring real-time server access, a need for increased network throughput, and slightly less functionality. A sort of hybrid architecture that incorporates the features of thin-client browser usage with a thick client exists in the form of a web-based LIMS.Some LIMS vendors are beginning to rent hosted, thin-client solutions as "software as a service
Software as a Service
Software as a service , sometimes referred to as "on-demand software," is a software delivery model in which software and its associated data are hosted centrally and are typically accessed by users using a thin client, normally using a web browser over the Internet.SaaS has become a common...
" (SaaS). These solutions tend to be less configurable than on premise solutions and are therefore considered for less demanding implementations such as laboratories with few users and limited sample processing volumes.
Another implementation of the thin client architecture that's offered is the maintenance, warranty, and support (MSW) agreement. Pricing levels are typically based on a percentage of the license fee, with a standard level of service for 10 concurrent users being approximately 10 hours of supports and additional customer service at $200 per hour. Though some may choose to opt out of an MSW after the first year, it's often more economical to continue the plan in order to receive updates to the LIMS, giving it a longer life span in the laboratory.
Web-enabled
A web-enables LIMS architecture is essentially a thick-client architecture with an added web browser component. In this setup, the client-side software has additional functionality that allows users to interface with the software through their device's browser. This functionality is typically limited only to certain functions of the web client. The primary advantage of a web-enabled LIMS is the end-user can access data both on the client side and the server side of the configuration. As in a thick-client architecture, updates in the software must be propagated to every client machine. However, the added disadvantages of requiring always-on access to the host server and the need for cross-platform functionality mean that additional overhead costs may arise.Web-based
Arguably one of the most confusing architectures, web-based LIMS architecture is a hybrid of the thick- and thin-client architectures. While much of the client-side work is done through a web browser, the LIMS also requires the additional support of Microsoft'sMicrosoft
Microsoft Corporation is an American public multinational corporation headquartered in Redmond, Washington, USA that develops, manufactures, licenses, and supports a wide range of products and services predominantly related to computing through its various product divisions...
.NET Framework
.NET Framework
The .NET Framework is a software framework that runs primarily on Microsoft Windows. It includes a large library and supports several programming languages which allows language interoperability...
technology installed on the client device. The end result is a process that is apparent to the end-user through the Microrosoft-compatible web browser, but perhaps not so apparent as it runs thick-client-like processing in the background. In this case, web-based architecture has the advantage of providing more functionality through a more friendly web interface. The disadvantages of this setup are more sunk costs in system administration and support for Internet Explorer and .NET technologies, and reduced functionality on PDAs and tablets.
LIMS configurability
LIMS implementations are notorious for often being lengthy and costly. This is due in part to the diversity of requirements within each lab, but also to the inflexible nature of LIMS products for adapting to these widely varying requirements. Newer LIMS solutions are beginning to emerge that take advantage of modern techniques in software design that are inherently more configurable and adaptable — particularly at the data layer — than prior solutions. This means not only that implementations are much faster, but also that the costs are lower and the risk of obsolescence is minimized.Standards covered by LIMS
A LIMS covers standards such as:- 21 CFR Part 11Title 21 CFR Part 11Title 21 CFR Part 11 of the Code of Federal Regulations deals with the Food and Drug Administration guidelines on electronic records and electronic signatures in the United States...
from the Food and Drug Administration (United States) - ISO/IEC 17025ISO/IEC 17025ISO/IEC 17025 is the main standard used by testing and calibration laboratories. Originally known as ISO/IEC Guide 25, ISO/IEC 17025 was initially issued by the International Organization for Standardization in 1999. There are many commonalities with the ISO 9000 standard, but ISO/IEC 17025 adds in...
- ISO 15189ISO 15189ISO 15189 Medical laboratories — Particular requirements for quality and competence specifies the quality management system requirements particular to medical laboratories. The standard was developed by the International Organisation for Standardisations's Technical Committee 212...
- Good laboratory practiceGood Laboratory PracticeIn the experimental research arena, the phrase good laboratory practice or GLP specifically refers to a quality system of management controls for research laboratories and organizations to try to ensure the uniformity, consistency, reliability, reproducibility, quality, and integrity of chemical ...
LIMS vendors
- Analytik JenaAnalytik JenaAnalytik Jena AG, based in Jena , is a provider of analytical, bioanalytical and optical systems for industrial and scientific applications. Analytik Jena was founded in 1990 as a sales and service company for analytical technology. The company has been listed on the Frankfurt Stock Exchange since...
- LabLynx, IncLabLynx, Inc.LabLynx, Inc. is a privately owned, funded, and managed American corporation that develops, supports, and markets laboratory information management system solutions. Its most well-known products include ELab, a browser-based LIMS, and webLIMS, a scalable hosted LIMS offered under the "software as...
- Labvantage
- MincomMincom LimitedMincom Pty Ltd is a software and services company providing business software to industries such as mining, public infrastructure, defense, oil and gas in more than 40 countries across North America, South America, Australia, South East Asia, Africa, and Europe.Mincom Inc. operates in North America...
- PerkinElmerPerkinElmerPerkinElmer, Inc. is an American multinational technology corporation, focused in the business areas of human and environmental health, including environmental analysis, food and consumer product safety, medical imaging, drug discovery, diagnostics, biotechnology, industrial applications, and life...
- Sapio SciencesSapio SciencesSapio Sciences is a software vendor that develops and markets the Exemplar product line. Exemplar is a versatile software tool that encompasses Laboratory Information Management, Electronic Laboratory Notebook, Cheminformatics and Data Management in a single framework.- Corporate History :Sapio...
- STARLIMSStarlimsSTARLIMS, an Abbott Company, develops and sells web-based commercial off-the-shelf Laboratory Information Management Systems ; Software solutions which manage the collection, processing, storage, retrieval and analysis of information generated in laboratories.- Corporate history :STARLIMS's initial...
- Thermo Fisher ScientificThermo Fisher ScientificThermo Fisher Scientific is a large life sciences supply company that was created in 2006 by the merger of Thermo Electron and Fisher Scientific.-Predecessors and merger:...
- The Weaver Group Inc.The Weaver Group- The Weaver Group :The Weaver Group is a private data management software company headquartered in Santa Monica, California. The company employs approximately 10 people, with customer and development facilities located in Fort Wayne, Indiana and Philippi, West Virginia.The Weaver Group markets to...
- Waters CorporationWaters CorporationWaters Corporation is a publicly traded laboratory analytical instrument and software company headquartered in Milford, Massachusetts. The company employs more than 5,000 people, with manufacturing facilities located in Milford, Taunton, Massachusetts; Wexford, Ireland; Manchester, England; and...