Industry Insights

LIMS vs ELN: What do I need?

Your biotech company is rapidly growing – you're ready for digital systems that will boost productivity, efficiency, and reproducibility, systems that will scale. But you may be wondering if you need a laboratory information management system (LIMS), an electronic laboratory notebook (ELN), or both.

LIMS vs ELN vs Benchling

To keep R&D workflows productive as your biotech company grows, you need digital solutions to help track experiments, samples, and reagents, quickly make sense of complex data, and streamline workflows. Because most individual software solutions (e.g., LIMS or ELN) are rarely equipped with all of these capabilities necessary to deliver the full benefits of efficiency and traceability, companies often adopt multiple software systems. Unfortunately, this can end up creating more headaches than insights, and choosing the best combination of options can be difficult.

But with Benchling, you get an all-in-one solution that is specifically designed for life sciences. It combines the capabilities of LIMS, ELNs, inventory management software, molecular biology tools, and more—giving our customers several advantages and helping them bring their products to market faster than ever before.

Let's go over a few common scenarios where LIMS and ELNs shine, and we’ll discuss how Benchling delivers the capabilities of both systems and more in a single solution.

LIMS vs ELN: I want to keep track of experiments


Electronic lab notebooks primarily let you find and track unstructured experimental records and data. All ELNs will track every addition and amendment to the records they maintain. This way you can easily explore the contents at any point in time, review any changes that were made, and see who made those changes. With some ELNs, you also get the benefits of entry templates to standardize how you document your experiments and digital search tools to locate specific entries.


Generally, LIMS are designed to manage structured, repetitive workflows. LIMS typically aren’t equipped with the features and flexibility needed to comprehensively and continuously maintain records for the wide-ranging experiments performed in the discovery stages of R&D. For this reason, LIMS are better at tracking structured workflows versus unstructured workflows, which ELNs are better at tracking. Modern LIMS are built to integrate seamlessly with ELN software to gain the benefits of both types of systems when it comes to tracking experiments and the resources needed to perform them.


Benchling is a cloud-based platform for life science R&D that delivers both structured and unstructured data capture by combining the capabilities of top-tier ELN and LIMS with other foundational informatics functions. When it comes to experiment tracking with Benchling, it is comprehensive, customizable, and seamless. You can link together entries, samples, and results that would normally be siloed in a standalone LIMS or ELN. With our customizable templates and tables for recording notes and results, as well as our advanced search tools, you can standardize how protocols and results are captured and filter your search results by parameters such as a cell line, plasmid, or other reagent used in the experiment. This allows you to see the complete, interconnected history of any experiment, drive reproducibility, and easily compare results.

LIMS vs. ELN: I want to keep track of biological samples and reagents


Some ELN software can integrate with or have basic built-in inventory management tools that link your research entries to your samples and reagents. While ELNs can help you to manage your samples and document your experiments, they are often limited in their ability to integrate with your entire instrument and software ecosystem, resulting in siloed data or clunky transitions as you progress through your experiment workflow.


Sample tracking is arguably the most basic capability of every LIMS, where you can assign each sample a unique identifier that can be linked to other entities and experiments. However, sample management with LIMS typically requires extensive customization to correctly connect entities and link relevant information in a way that increases efficiency. This is because “sample” can mean different things to different labs. Proteins, cell lines, plasmids, miRNA, and oligonucleotides are just a few of the types of samples a given lab might need to manage, and each of these entities has distinct relationships to each other, as well as specific types of data that must be associated to them.

Most LIMS were originally built for small molecule R&D workflows and have trouble handling diverse molecular biology sample types without extensive customization. This can result in long setup times and expensive reconfigurations as biotech companies grow.


With Benchling, you get the same sample and inventory management capabilities that ELNs and LIMS can deliver, but in an easily configurable, cloud-based platform that is built to properly manage the full range of samples a modern lab might encounter, such as plasmids, proteins, cell lines, and small molecules.

Without writing a single line of code or involving vendors, designated administrators can digitally model any entity, automatically interconnect DNA and protein constructs, and structure parent/child relationships to track entity lineages. You can even create an entry in Notebook (the Benchling application for recording experiments) and link that entry to specific samples, plasmids, cell lines, and other reagents that are tracked in the Benchling Registry application. All of this happens in one seamless platform, with no need to close, open, and tab between distinct modules.

LIMS vs ELN: I want to connect DNA sequences to downstream results


Companies need digital solutions that enable them to connect the dots between results as samples transition through the R&D workflow. For instance, having software that helps you quickly understand which constructs have the best expression can improve productivity and generate insights faster. In life science R&D, multiple teams are often involved in performing different phases of a given project. With an ELN, you can keep information from multi-day and multi-person studies organized together, making it easier for any team member to tie experimental protocols to results and to pull together data for analysis. While an ELN can help keep your notes and results organized and streamline knowledge transfer as projects are handed off, you may need additional software or a more sophisticated ELN with built-in analytical tools to draw connections between results and DNA sequences.


While LIMS are very sample-centric, most of them are built to handle small molecules rather than modern molecular biology samples. LIMS typically excel at capturing information relating to a given sample and what happens to it, such as what tests it will undergo, related reagents and instruments, and derivatives of the parent sample. However, this is more difficult for a LIMS to do in a modern life science environment where labs need to view, manipulate, and compare DNA and protein sequences.

These limitations become even more apparent when trying to capture the metadata and details of experiments involving a specific sample, such as how a certain variant impacted receptor binding and how it compares to other variants. To gain these capabilities, life science R&D labs need functionalities that conventional LIMS often fail to deliver. Connecting samples or specific DNA sequences with data and analysis files, which may be simple text files, may require integration with a third party software such as a top-tier ELN that has capabilities that can easily bring results from separate experiments together.


With Benchling, you can gain scientific and operational insights at a speed that a typical ELN and LIMS cannot deliver. The beauty of Benchling is that it is built to handle diverse molecular biology samples (and all the complex information that comes with it), while also unifying your instrument and software ecosystem through codeless configurations and seamless integration. Unlike ELNs and LIMS, Benchling has a built-in Molecular Biology application where you can easily view, manipulate, and compare DNA, RNA and protein sequences. And because it is part of our unified platform, you get end-to-end traceability of all your sequences. You can easily see the downstream samples and results that any sequence has led to. For example, view the binding affinity of all antibody lots with a given light chain variable fragment.

This unification simplifies data analysis and insight generation by assembling critical information and ensuring that all the information you need—the protocols, the results, and the plasmids, strains, and other reagents—is readily available and up-to-date. You can automate data recording from instruments into a single data warehouse. You can create an entry in Notebook, the application for recording experiments, and automatically link that entry to specific samples, plasmids, cell lines, and other reagents that are tracked in the Registry application. Then on the same platform, analyze different runs of the same experiment at the DNA sequence level using customizable dashboards.

“What Benchling gives us most of all is speed. It allows us to process more [NGS] samples and generate that data more quickly so that we can make decisions faster.”

—Bob Gantzer, Head of Lab Automation & Robotics @ Beam Therapeutics

LIMS vs ELN: I want to make IND filings and regulatory audits easier


ELNs help keep experiments and results organized and readily accessible through entry templates and search features, and can also have more specific features that make regulatory reporting, IND filings, and compliance audits more efficient. While typical ELNs are developed for flexible environments, some include features well-suited for regulated environments (e.g., 21 CFR Part 11 compliance). These features can include custom witnessing and review processes with electronic signatures, audit trails recording the review process step-by-step, and automatic version history tracking.


These systems provide centralized access to quality control data. For labs that need to meet specific regulatory requirements, LIMS can provide audit trails for samples and data as well as quality control and quality assurance information.


Benchling provides LIMS reporting functionality that can help you efficiently prepare for regulatory audits and deliver insights. You can meet regulatory requirements with application controls such as locking electronic signatures, restricting user access, and strict versioning of all edits for audit trails. Quickly and efficiently respond to auditor requests with comprehensive, standardized digital records (including 21 CFR Part11 compliance). Easily reconfigure and update Benchling to meet the changing needs of evolving organizations.

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