Laboratory information management system
Sometimes referred to as a laboratory information system (LIS) or laboratory management system (LMS), a laboratory information management system (LIMS) is a software-based laboratory and information management system 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 integrated application that handles both laboratory management and enterprise resource planning processes, from testing to marketing.
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: the definition of a LIMS will shift based on who you ask and what their vision of the modern lab is. 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 term "LIMS" has tended to be used to reference informatics systems targeted for environmental, research, or commercial analysis such as pharmaceutical or petrochemical work. "LIS" has tended to be used to reference laboratory informatics systems in the forensics and clinical markets, which often required special case management tools. The process development execution system or "PDES," while having similar functionality in some ways, has generally applied to a wider scope, including, for example, virtual manufacturing techniques, while not necessarily integrating with laboratory equipment.
In modern times, LIMS functionality has spread even farther beyond its original purpose of sample management. Assay data management, data mining, data analysis, and the integration of electronic laboratory notebooks (ELNs) and third-party applications are all features that have been added to many LIMS, enabling the realization of translational medicine completely within a single software solution. Additionally, the distinction between a LIMS and a LIS has blurred, as many LIMS now also fully support comprehensive case-centric clinical specimen and patient data management.
History of LIMS
Up until the late 1970s, management of laboratory samples and their associated analysis and reporting was a 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 through LIMS-related conferences. By 1988, the second-generation commercial offerings were tapping into relational databases to expand LIMS into more application-specific territory, and international LIMS conferences were in full swing. As personal computers 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 networking capabilities and georeferencing of samples, to the adoption of XML standards and the development of internet purchasing.
By the early 2010s, some LIMS had added additional characteristics that continued to shape how a LIMS was defined. Examples include the addition of clinical functionality and electronic laboratory notebook (ELN) functionality, as well a rise in the cloud-based software as a service (SaaS) distribution model. By the late 2010s, cloud-based LIMS were more numerous in quantity and adoption but not the de facto standard, as the costs and daunting nature associated with vendors transitioning legacy products to the cloud and with companies trying to integrate a cloud-based LIMS into a complicated IT environment have partially stymied growth. Despite these challenges, market research companies such as Markets and Markets believe that cloud-based version of the LIMS will see the highest growth rate in the coming years, citing "on-demand self-serving analytics, ease of use, affordability, reliability, no upfront capital investment for hardware, adaptability & flexibility, and a pay-as-you-go pricing model" as primary drivers.
Laboratory information management operations
The LIMS is an evolving concept, with new features and functionality being added often. As laboratory demands change and technological progress continues, the functions of a LIMS will likely also change. Despite these changes, a LIMS tends to have a base set of functionality that defines it. That functionality can roughly be divided into five laboratory processing phases, with numerous software functions falling under each:
- the reception and log in of a sample and its associated customer data;
- the assignment, scheduling, and tracking of the sample and the associated analytical workload;
- the processing and quality control associated with the sample and the utilized equipment and inventory;
- the storage of data associated with the sample analysis; and
- the inspection, approval, and compilation of the sample data for reporting and/or further analysis.
There are several pieces of core functionality associated with these laboratory processing phases that tend to appear in most LIMS.
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 barcodes to affix to the sample container. Various other parameters such as clinical or phenotypic information corresponding with the sample are also often recorded. The LIMS then tracks chain of custody (CoC) 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 also 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 often create LIMS that are adaptable to individual environments. This typically involves the inclusion of workflow management tools in the LIMS. Users may also have regulatory concerns to comply with such as CLIA, HIPAA, good laboratory practice (GLP), 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 system is required for rigorous tracking of field-level changes to LIMS data.
Instrument and application integration
Modern LIMS offer integration with laboratory instruments as standard. 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.
In addition, a LIMS typically allows for the import and management of raw assay 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, a dozen 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.
Increasingly, a LIMS also provides the ability to integrate with third-party applications such as enterprise resource planning systems or regulatory compliance systems (such as seed-to-sale reporting systems for cannabis testing). This integration is typically achieved through the use of an application programming interface (API), code which serves as an interface between different software programs and facilitates their interaction.
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 exchanges. 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 mobile and other third-party applications integrate with the LIMS. The successful transfer of data files in a wide variety of formats, while maintaining the associated metadata and keeping it secure, is paramount. Historically speaking, the transition "from proprietary databases to standardized database management systems such as Oracle ... and SQL" has had significant impact on how data is managed and exchanged in laboratories, culminating today in cloud-based relational and NOSQL databases that can be set up, operated, and scaled with relative ease.
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 management
- fully track and maintain an audit trail
- barcode 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
- 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 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 workflow; reports
- create and schedule reports in a specific format; schedule and distribute reports to designated parties
- time tracking and performance assessment
- calculate and maintain processing and handling times on chemical reactions and workflows while assessing analyst, instrument, or test performance
- data mining
- search a wide variety of data repositories and their associated metadata to make and improve on research insights
- invoicing and sales
- provide an integrated structure to bill clients directly and track sales activity
LIMS architecture and delivery methods
A LIMS has utilized many architectures and distribution models over the years. As technology has changed, how a LIMS is installed, managed, and utilized has also changed with it.
The following represents architectures which have been utilized at one point or another:
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 also provided 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 browser. The thick-client LIMS can become web-enabled through an add-on component.
A web-enabled 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.
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 installation exists in the form of a web-based LIMS.
Additionally, maintenance support and warranty (MSW) agreements are usually offered with thin-client installations. 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 support and additional customer service at a set per-hour rate. 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.
Cloud and SaaS
In the early 2010s, LIMS vendors began to rent hosted, thin-client solutions as "software as a service" (SaaS). These cloud-based solutions tended to be less configurable than on-premise solutions and were therefore considered for less demanding implementations such as laboratories with few users and limited sample processing volumes. However, cloud-based software has seen greater adoption as the technology has improved, and configurable LIMS for laboratory operations big and small have become a more realistic option.
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's .NET Framework 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 mobile platforms.
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. The technology of LIMS solutions has improved as software design methodologies have improved, however, and many more configurable and adaptable options exist than previously. This means not only that implementations are much faster, but also that the costs are lower and the risk of obsolescence is minimized.
The distinction between a LIMS and a LIS
Historically, the LIMS and LIS have exhibited a few key differences, making them noticeably separate entities:
1. A LIMS traditionally has been designed to process and report data related to batches of samples from biology labs, water treatment facilities, drug trials, and other entities that handle complex batches of data. A LIS has been designed primarily for processing and reporting data related to individual patients in a clinical setting.
2. A LIMS needs to satisfy good manufacturing practice (GMP) and meet the reporting and audit needs of the U.S. Food and Drug Administration and research scientists in many different industries. A LIS, however, must satisfy the reporting and auditing needs of hospital accreditation agencies, HIPAA, and other clinical medical practitioners.
3. A LIMS is most competitive in group-centric settings (dealing with "batches" and "samples") that often deal with mostly anonymous research-specific laboratory data, whereas a LIS is usually most competitive in patient-centric settings (dealing with "subjects" and "specimens") and clinical labs.
However, these distinctions began to fade somewhat in the early 2010s as some LIMS vendors began to adopt the case-centric information management normally reserved for a LIS, blurring the lines between the two components further. Thermo Scientific's Clinical LIMS was an example of this merger of LIMS with LIS, with Dave Champagne, informatics vice president and general manager, stating: "Routine molecular diagnostics requires a convergence of the up-to-now separate systems that have managed work in the lab (the LIMS) and the clinic (the LIS). The industry is asking for, and the science is requiring, a single lab-centric solution that delivers patient-centric results." Abbott Informatics Corporation's STARLIMS product was another example of this LIMS/LIS merger. With the distinction between the two entities becoming less clear, discussions within the laboratory informatics community began to includes the question of whether or not the two entities should be considered the same. As of 2017[update], vendors continue to recognize the historical differences between the two products while also continuing to acknowledge that some developed LIMS are taking on more of the clinical aspects usually reserved for a LIS.
Standards affecting LIMS
A LIMS' development and use is affected by standards such as:
- Title 21 CFR Part 11 from the Food and Drug Administration (United States)
- ISO 17025
- ISO 15189
- Good laboratory practice
See the LIMS vendor page for a list of LIMS vendors past and present.
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This article is a direct transclusion of the LIMSwiki article and therefore may not meet the same editing standards as CannabisQAwiki.