Laboratory Software – Which is the Right One for Our Lab?

by | 02. 02. 2021 | Laboratory digitalization

Reading Time: 8 minutes

There are different types of laboratory software that we know today. They range from simple applications to very sophisticated software that manages complex processes. Not all software fits into every laboratory, and selecting the right tool can be a complicated and long process. Sometimes laboratories decide to stay with their old system (usually a combination of paper, some basic computer programs, and local storage) rather than digitalizing their processes and investing time into new software implementation or new laboratory information system. That is a step back, though. Laboratory software can increase the efficiency and productivity of a laboratory, and provides better inventory management. Furthermore, it guarantees the traceability of processes and data security, which is crucial if you aim to achieve data integrity. In this article, you will learn more about different types of laboratory software solutions, what are their typical features, and where do they fit.

Electronic Lab Notebook (ELN)

An ELN replaces paper notebooks and is used during the R&D process. It gives a better overview of data, with the ability to search, share, collaborate and organize in a single platform. It is also more secure, and it takes less space than paper notebooks. The use of ELNs as a lab equipment is still in its early days – Kanza et al. in 2017 found that 11% of participants are actively using ELN, and 76% are about to implement it in the following years or next decade. Modern ELNs span beyond their basic functionality and help scientists to be more efficient. Most ELNs can be used on tablets and therefore, can also be brought to laboratories. If you are choosing an ELN for your medical laboratories or clinical lab, you should read The 9 best ELN for your laboratory.

ELNs are, therefore, universal research data management platforms. They hold data about protocols, raw data, analysis protocols, analyzed lab data, results, figures, and reports. It also helps to track inventories and equipment, and improve operational efficiency and workflow management. Important features are also collaboration, sharing, and automating processes. ELNs usually also supports integrations with other software, which allows them to become a central data storage point for R&D operations. Data can be automatically fetched from laboratory instruments and fed to analysis software. All of this while maintaining integrity and history of changes.

SciNote ELN - Electronic Laboratory Notebook

Example of an electronic laboratory notebook – SciNote

The industry widely adopted ELNs and uses them instead of paper notebooks. ELNs, therefore, implement also features needed by 21 CFR Part 11 (and equivalent) regulations. Examples of such key features are electronic signatures, audit trails, and access control. ELNs are accepted by the courts as an equivalent to paper notebooks and are treated equally in patent disputes.

Example: Fiona, a PhD student, is about to perform an assay. She first finds the protocol in the group repository of protocols in research group ELN and copies it to her workspace. Then, she makes some changes and sends it to her supervisor to review it. After the supervisor confirms it, she goes to the laboratory and performs the assay based on her lab data. The electronic lab notebook guides her through the protocol, and she can sign off each step of the protocol. Then she uploads the raw data to ELN, analyzes it with the analysis pipeline attached to the protocol, and saves the analyzed data next to the raw data. Then she sends the results for review to the supervisor. The supervisor is happy with the results and approves them. The supervisor can also electronically sign the experiment, preventing any further modifications to it. Based on the confirmed and signed results, Fiona can start working on her lab reports.

Laboratory Information Management System (LIMS)

LIMS systems are commonly used in routine analytical laboratories, where the process is focused on samples. The system tracks samples and their related metadata, as well as the analyses that need to be done and the results of analyses. Laboratory information management system as a lab equipment uses several tools that simplify the process, automate processes and ensure integrity, such as barcode scanners, label printers, and integrations with other relevant databases, for example, hospital information systems.

Key features are also related to data integrity. They support audit trails, access controls, and electronic signatures. They comply with 21 CFR Part 11 requirements and are therefore commonly used in GMP, diagnostic labs or diagnostic centers, clinical labs, and medical laboratories (for usage of medical records and improved patient care). An important feature is lifecycle lab management. This means that the analyses, results and lab reports go through a process of electronic signage and reviewing by reviewers and managers. The integrity is further improved by tight integration with laboratory instruments. Laboratory information management software can directly manage the laboratory instrument and fetch data and other relevant information, and therefore enable easy access to relevant data. Then it automatically analyses it and generates a report for the physician. Tight integration of laboratory instruments practically eliminates human intervention and therefore ensures data retain their integrity. LIMS software can also be integrated with other systems, such as ELNs, electronic medical records (EMR) for medical laboratories, health information systems (HIS), or enterprise resource planning (ERP).

The best-known LIMS systems are SampleManager, LabWare, and STARLims. There are hundreds of others laboratory management systems on the market. There are also many guides on how to choose the LIMS system for your lab operations, such as the one published at LabManager.

Example: In healthcare and pharmaceutical organizations, the manufacturing is planned in ERP. This reserves resources at the appropriate times, so there is no waiting times. After the manufacturing, the samples are taken to Quality Control (QC) laboratory, where the analyses are synced between LIMS and ERP. LIMS then issues a certificate of analysis and sends it back to ERP.

You read more about our completed digitalization strategy for implementing LIMS or ELN system in this use case.


BioSistemika offers vendor-independent consulting services, leveraging extensive expertise in LIMS and ELN selection. Our diverse interdisciplinary team, comprised of professionals with backgrounds in health and life sciences, delivers impartial guidance customized to your specific needs.

Reach out to us for a consultation on how we can support you in identifying the ideal LIMS or ELN solution for your laboratory.


Laboratory Data Management System (LDMS)

LDMS is like cloud storage for laboratories. Besides research data, it also stores relevant metadata and therefore makes data searchable. Key features are also access control, electronic signatures, audit trails, lifecycle management, integrated provider portal, and collaboration features. ELN and LIMS systems integrate nicely with LDMS and can use it as backbone storage. They are less commonly used and are being actively replaced by ELNs.

Chromatography Data Management System (CDMS)

CDMS (also referred to as CDS) is an LDMS with additional key features specific for the lab management of chromatography systems and data analysis. These systems are usually cloud applications with local clients. The central server has control over all chromatography systems and allows remote control and data analysis. Therefore most of the work can be done from users’ local PC.

The basic component of CDMS is the chromatography toolkit. It helps users during the method development, validation, data analysis, and report generation. It also implements features regulated by 21 CFR Part 11, such as access control, audit trails, electronic signatures, and lifecycle management. This allows the use of these instruments in GMP environments. CDMS has many organizational features. Therefore, an organization usually has a single CDMS system that is used by many departments. It integrates with the LIMS system and provides a complete data accuracy cycle.

Market leaders in CDMS are Chromeleon, Empower, Analyst, Xcalibur, and MassHunter.

Example: An R&D department in a biotech company would use a CDMS to create methods and analysis pipelines for chromatography assay. After the methods and pipelines are validated, they go through a review lifecycle, where other scientists review them and sign reports. After that, the method cannot be changed. Then the method is transferred to the production laboratory for routine use.

Laboratory Execution System (LES)

LES is used to support the execution of processes according to standard operating procedures (SOP). A laboratory workstation would have a computer system (PC or tablet) with all necessary details to perform a process according to SOP. The laboratory operator would need to sign-off each step. Most LES features are today available in ELNs or LIMS software.

Process Analytical Technology (PAT) Software

Biotechnology production has become a dynamic process with online quality control and performance measurement systems. PAT is the software that manages the online control systems and adjusts the production parameters in real-time. PAT’s backbone are the algorithms that accept analytical data and execute amendments to the production system, ensuring the desired quality standards. PAT software is usually custom-built or adapted for each system.

Automation Scheduling Software

This type of software is used for controlling laboratory automation systems. Automation offers a number of advantages, such as higher efficiency and more robust laboratory assays. The software is used to design the automation process in an easy way, execute it and control the automation hardware. It also integrates with LIMS or ELN to store the protocols and results in a timely manner. Automation schedulers are usually developed and supplied by the vendors of the automation workcells.

Laboratory Instrument Software

The first software in the laboratories was software that came with laboratory instruments. This software is used to control the instruments and analyze the data. Historically, these have been desktop applications, but today there are some ventures into cloud as well.

Instrument software often lags in user experience, which can impact user adoption. The vendors are increasingly more aware of this, and we can see advances. Among the technical features, there is a trend of integration with other software, ELN or LIMS. Some vendors are also providing their cloud platforms, which are handy when there is an ecosystem of instruments.

Middleware and Robotic Process Automation (RPA)

Middleware is an application that sits between two other applications and facilitates integration between them. Laboratory middleware takes care of data exchange between different systems, such as instruments, ELN, LIMS, and data analysis applications. Laboratory middleware is usually a platform that needs to be customized for a specific laboratory. This results in high costs of implementation. This could be simplified with higher adoption of laboratory data standards, such as SiLA and AniML.

RPA is a type of software used for automating repetitive computer tasks, freeing up laboratory technicians’ time. It is often used in automated testing of applications, but recently it is used for business processes as well. RPA can be programmed in a way to perform the function of laboratory middleware. More importantly, it can be used for follow-up data processing, such as data extraction, data formatting, and reporting. The benefit, besides higher efficiency, is also maintenance of data integrity throughout the whole process, which eliminates the need for additional integrity reviews and ensures data security. Best known commercial solutions are UIPath, Blue Prism, and Automation Anywhere. Notable open-source solutions are Robotic Framework Foundation, TagUI, and Taskt.

Data Analysis Software

Data analysis software is used for the analysis and summarization of data. The results are then imported in the reports. This is often called last-mile analytics. Data analysis software can be intended for general use, such as spreadsheets and statistical packages (R, SPSS, Orange, Knime). There are also assay-specific packages and platforms, for example, for next-generation sequencing. The tools range from command-line tools to desktop applications and server platforms. An example of an open-source solution is Chipster.

Enterprise Resource Planning (ERP)

ERP is a type of software used for planning and management of supply chain, services, manufacturing, finances, and other processes within the organization. They are often used throughout organizations and therefore also in laboratories. Laboratory managers can use it for procurement, inventories, supply chain management, and services management. There are many vendors on the market, such as Oracle, SAP, Sage, and Microsoft.

How to choose the right laboratory software?

Laboratory software is a complex landscape. Some choices are obvious, such as lab automation software or instrument software. On the other hand, choosing between ELN, LIMS, or whether to use any of those lab management software solutions at all can be difficult.

A good approach is to map your business processes first and identify the type of data and processes that you deal with. Usually, ELN is needed in almost any type of laboratory – medical labs, clinical labs, and others. It acts as a central repository of protocols and reagents. Also, any R&D work is recorded in it. Besides electronic lab notebook, you might also need LIMS if you process many samples in a routine way, such as in QC or diagnostic laboratory. In addition, LIMS can be integrated with other lab management software solutions, such as electronic medical records (EMR), health information systems (HIS), or enterprise resource planning (ERP).

The other choices of software solution then truly depend on your business and manual processes.

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