How does a LIMS work?

How does a LIMS work? | LabLynx Resources

Earlier pieces in this series looked at what LIMS and ELNs are[1] and compared two different methods of implementing a LIMS (on-premise vs the cloud)[2].   This article is going to dive deeper into LIMS and look at both how it works and also improves lab operations.  We’ll do that by looking at one type of service testing lab as an example – a water quality testing lab – and seeing how the components of a LIMS can improve its operation.  Because service testing labs have many common functional characteristics, it should be easy to translate this material to your lab’s needs.

Service testing labs are scientific facilities whose primary purpose is to perform testing on samples that are submitted by an outside group.  Examples include quality control, contract testing labs, analytical & physical research testing, clinical labs, etc.  One thing they have in common is their operational and behavioral structure.  They are similar to any service operation that carries out customer requests:  those requests have to be logged in, work scheduled, priorities identified, tasks completed and the client notified of the results and billed.

Water testing labs offer a variety of testing services to residential and industrial customers.  Those tests can include those in the following table, as well as many others.

These tests may be grouped into common sets of testing or they may be requested individually.  For example, clicking on “Well Maintenance” testing would automatically assign testing for Bacteria, Nitrates, Turbidity & Color, and both Basic & Comprehensive Water Chemistry tests to the sample[1].  The point is this: there are a lot of options to keep track of and a LIMS does that for you.

Let’s assume that you are the manager of a water testing laboratory; how would a Laboratory Information Management System assist your lab’s operations?

The Sample Enters the Lab

Several things have to happen:

  • The sample has to be logged in,
  • Have tests assigned to it,
  • Priorities set,
  • The storage location is chosen, and
  • Aliquots are drawn if needed.

In a manual operation, all of this is labor-intensive and may require a full-time person in a high-volume facility.  Using a LIMS is a matter of filling in a few elements on the screen, a few clicks to choose testing, priorities, and assigning a location for the samples.  Should the client request a standard set of tests, just click on the set identifier to complete that process. If this is a current client the contact and billing information can be selected from a contact list.  If the customer warrants it, they can be given carefully controlled access to the LIMS to log samples in; once the samples arrive in the lab the LIMS is updated and the work is ready to proceed.  Batch log-ins (several samples with the same testing requirements) can be enabled to streamline the process even further.  The process can be further facilitated with the use of barcodes, and have sample labels produced as the material is cataloged.

Customers with large, routine sample submissions can be provided with standardized sample containers and the ability to print sample labels, streamlining the sample submission process, making it more convenient for the customer and reducing the workload for the lab.  The customers participation could reduce the cost/test for those clients.

Determining the Work to be Done

An analyst is preparing to run a set of tests and needs to know what samples have to be processed, and whether or not there are any high priority requests.  Manually, this is a paper chase, checking log-in entries, looking for samples, and the sample request forms as someone else might be working on other tests for the same materials.  Using a LIMS, it’s a matter of generating a worklist that contains the sample IDs (with aliquots if any), priorities, sample locations and comments.  When the work is completed, that same worklist can be used to enter the test results.

If the analysis is being performed is done with an instrument supported by a computer system (instrument data system – IDS), the worklist can be sent to the IDS. When the work is done the worklist plus results can be sent back to the LIMS for automatic data entry.

LIMS has facilities for data review, both automatic (based on preset acceptable ranges), and manual to catch results that are questionable and need attention.

Results Review, Approval and Reporting

As noted results review facilities are built into the system making it easy to flag questionable values and take corrective action.  This is an important component of the system’s contribution to data integrity and the confidence you would have in releasing results to the client.  Once final approval and sign-off are completed, a report can be generated that can be printed or emailed to the client depending on their preferences.  The billing department can be given limited access to the LIMS to find out what work should be charged.

Sample Tracking vs a Full LIMS

The description above is that of the sample tracking functionality of a LIMS, and when the products were first introduced that was the extent of their capability.  As such, they provided a major improvement in the effectiveness of lab operations.  Reducing the need for clerical staff, making it easier to find information needed to conduct work, and using connections between instrumentation and the database system for data entry, all contributed to a positive return on investment.  The benefits of the software tool to your lab didn’t stop there as vendors continued to enhance product capabilities.

The primary purpose of a testing lab, in this case, a water quality test facility, is to produce data and information (D/I) about the samples that are submitted, making the contents of the data system a very valuable property.  Maintaining that value is a fundamental lab goal.

The quality of that D/I is governed by the reliability of the procedures used, how they are executed, and your ability to organize and work with them.  Paper-based systems, even spreadsheets tend to fail with large datasets when faced with the questions: how do I know that data is accurate and hasn’t been tampered with?  How does your data organization contribute to Data Integrity?

Moving Beyond Sample Tracking

Data Integrity is a subject that is high on the FDA’s list of concerns as well as Good Manufacturing Practices, and should be for every industry: decisions are being made based on D/I; how reliable is it?  Does it meet the ALCOA-CCEA[2] framework requirements?  The letters[3] stand for Attributable, Legible, Contemporaneous, Original, Accurate, Complete, Consistent, Enduring, and Available.  Although there is nothing in the framework that requires an electronic implementation, meeting that specification with a paper-based system would be difficult.

Among the features a LIMS provides is an automatic audit trail facility.  Any change must be accounted for with the original value preserved, a reason for the change provided, and the editor identified.  This plus a chain-of-custody facility provides support for both regulatory compliance and preserving Data Integrity.

Instrument Calibration and Maintenance is another outgrowth of LIMS development.  Not only do you have to ensure that procedures are executed properly, but as a manager, you also have to provide proof that the equipment and reagents used are up-to-date and in good working order.  That is what this section of the software provides for you.  It is both a record of past maintenance activities and a calendar of upcoming calibration and preventive maintenance work.  If there is any question about the suitability of equipment for a procedure, this data will address it.  Along with that module, we have available an inventory and equipment management system.  Between the two you have:

  • Equipment Scheduling and Availability Status,
  • Logs of Equipment Issues for Malfunctions and Errors, and
  • Performance Tracking.

Sample Location Management

Keeping track of the physical location of samples (and aliquots) can be a major headache in lab management.  If it isn’t done with care and attention your analysts can waste a lot of time looking for materials they have to work with.  We’re not talking about a few dozen or hundred samples, a medium to large lab may have thousands and each may have its ow disposal requirements.  One example from Life Sciences is Biobanking.

Biobanking[4] refers to the collection, storage, and management of potentially tens of thousands of samples of biological fluids and tissue samples for research purposes.  The sample consists of two parts: a description of the source and the physical material itself.  Depending on the stability of the material and the effect of freezing, samples may be kept at room temperature or in low-temperature freezers at -80° C.  Samples may be divided – split – and stored in different locations to prevent the failure of a storage device from destroying the entire sample.  All of the descriptive information, test results, and location information about the samples would be stored in the LIMS.  This type of storage information management will grow in importance as we move to automated retrieval of samples for testing.

Personnel Management

A lab-wide information management system should include information about laboratory personnel including:

  • Personnel records – emergency contact information (both family and medical), allergies, biological/chemical sensitivities, and dietary issues that would be useful when planning travel or events,
  • Scheduling – travel, vacations, holidays, sick days,
  • Training/educational information – formal courses, online, short courses, and certifications including procedural & equipment certifications. The latter point ties back into support for Data Integrity Programs.

Instrumental Data/Information Collection

We noted this earlier.  This is one of the features that sets a LIMS apart from other database systems, and why working with a commercial LIMS product is preferable to build-your-own or adapting software that appears to act like LIMS.  If your lab is all about producing data and information, then streamlining the process of entering it into the data system is a major consideration.  LIMS systems were built to connect to instrumentation ranging from pH meters and balances to high-end instrumentation each with its computer (IDS) for collecting and processing data.  That link is usually bi-directional.  Simpler devices may use a command/response structure to initiate actions (for example, take a pH measurement) with another to send it to the LIMS.  Often this is done via “middle-ware”, systems that handle the details of the experimental procedure and converse with the device, and then reformate the message protocol to something a networked LIMS can handle.  An IDS does this for you automatically.  The IDS’s communications can also include the downloading of worklists (a list of samples that need to be processed and the test IDs) and when the work is completed, return that file with the results so that they can be entered into the appropriate data fields for those samples.  The vendors build these facilities into the LIMS because they understand how labs work and what the requirements are to improve performance.  The software is continually updated to ensure that it works with updated/new systems, providing the testing & validation needed to ensure that your lab meets regulatory guidelines and requirements.

Having an IT group, one that may not be familiar with lab instrumentation and IDS, can compromise the entire LIMS project and miss important functionality requirements.

LIMS as the Operational HUB of Your Laboratory

Since the early days of LIMS product development, the software has become easier to implement in both on-premise and cloud-based versions; the latter being easier and faster to put into service.  The benefits of the software system include:

  • Centralized management of all lab information – data and information are the products of lab work and having a LIMS provides the central organizational focus will allow you to gain more value from the lab’s work, provide faster response to questions, and offer better/more effective services to your clients.
  • More efficient and effective operations with better organization of work execution.
  • Control over documents and procedures. For example, no confusion over what the current version of the lab procedure is.
  • Reduced operating costs, increased revenue (contract labs), and better return on investment.
  • Better control over consumables, and resources. Equipment will be up-to-date and its status as available for use won’t be in question.
  • More effective communications with clients.
  • The systems will grow and adapt to changes in the lab’s operations.

Not only will the LIMS act as a hub for the lab, but it will also provide a point of data/information transfer to corporate ERP systems, Electronic Lab Notebooks in research, and plant management in production operations.  Putting a LIMS into service to support your lab will reduce the clerical workload, eliminate the paper-chase looking for results, and put all the lab’s information and final results at your fingertips.  In short, higher productivity at a lower operating cost.

Learn how you can start optimizing your lab’s operations today by clicking here, or reach out to our team at [email protected].




[3] UGA Extension “Testing for Water Quality”,inorganic%20and%20organic%20chemicals%20tests.&text=Bacteriological%20tests%20generally%20check%20for,absence%20of%20disease%2Dcausing%20bacteria.

[4] If you aren’t familiar with the term type it into your favorite search engine, one good summary can be found at

[5] ALCOA was the original framework that was extended to ALCOA-CCEA


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