How to Choose the ELN System Your Lab Actually Needs

Choosing an ELN system (electronic lab notebook) can easily turn into a feature comparison exercise: long spec sheets, similar-sounding demos, and a lot of open browser tabs. But the best ELN software for your lab isn’t the one with the most features. It’s the one that quietly supports how your team already works, while helping you reduce risk and move faster.

Instead of asking, “Which ELN system is the most powerful?”, a better question is, “Which ELN system do we actually need?” This guide walks through how to answer that.

Contents:

• Start with Why
• Map Lab Workflows Before Features
• ELN System Requirements Checklist
• Evaluating Usability
• ELN as Part of You Data Ecosystem
• ELNs Decision Framework
• LabKey’s ELN

 

Start With Why You Need an ELN System

Before you compare vendors, get clear on why you’re looking for an ELN system in the first place. Most labs see similar triggers:

• Experimental records scattered across paper notebooks, personal drives, or email
• Confusing version histories for protocols and results
• Increasing pressure from auditors, sponsors, or collaborators
• More remote or hybrid work, making it harder to stay aligned

If you skip this step, it’s easy to select an ELN system that looks impressive in a demo but doesn’t solve your core problems.

Take an hour with a few key people in the lab and write down three to five concrete, measurable goals. For example:

• Cut time spent on documentation by 30%
• Reduce repeated experiments due to missing or unclear records
• Make it possible for a new team member to find any protocol or result in under two minutes
• Be “audit ready” for a specific standard or sponsor at any time

These goals become your filter. When you evaluate an ELN system later, you’re not just asking, “Does it have this feature?”, you’re asking, “Does this help us hit our goals?”

 

Map Your Lab’s Workflows Before You Map Features

An ELN system is only as effective as its fit with your real workflows.

Start by documenting a few typical experiment flows end-to-end:

• How a study or experiment is planned
• How protocols are created, shared, and revised
• How data is captured (instruments, uploads, manual entry)
• How results are reviewed, approved, and reported

Include who does each step and what tools they currently use (paper, spreadsheets, shared drives, existing software).

Then, identify where an ELN system should replace current habits versus just mirror them:

• Replace: manual transcriptions, duplicate data entry, email-based approvals
• Mirror (at least initially): naming conventions that already work, key templates your team relies on, approval paths that are required by SOPs

If you understand your workflows first, you can look at an ELN and say, “This fits our process with manageable adjustments,” instead of “We’d need to completely rethink how we work to use this.”

 

ELN System Requirements Checklist (People, Not Just Features)

Most requirements lists for an notebook start with ELN features. A more reliable approach is to start with the people who will use the system every day and what they need to accomplish. That people-first view keeps your requirements grounded in real work instead of abstract capabilities.

User types and access levels

List the different user types in your lab and what they need:

• Bench scientists and analysts
• Lab managers or directors
• QA/RA staff
• External collaborators (CROs, academic partners, core facilities)

For each role, ask:

• What do they need to do in the ELN system day-to-day?
• What do they need to see, and what should be restricted?
• How often will they actually log in?

This helps you define role-based permissions and check whether an ELN system can support your real access model, not just a generic one.

Template needs and standardization

Think about the kinds of work your lab does repeatedly, such as

• Core assay types
• Standard protocols and SOPs
• Common calculations and derived metrics

Your ELN system should make it easy to:

• Create and maintain standardized templates
• Lock what needs to be controlled (e.g., critical steps in an SOP)
• Leave room for flexibility where experiments are still exploratory

If templates are hard to build or update, the ELN will quickly fall out of sync with how your lab actually operates.

Collaboration needs

Finally, consider how your ELN needs to support collaboration:

• Do multiple teams need to work on the same projects or experiments?
• Do you regularly involve CROs or external partners who need controlled access?
• Do you need fine-grained sharing (e.g., share a project or folder, not an entire notebook)?

 

Evaluating ELN System Usability and Adoption Risk

You’re not just buying an ELN system. You are choosing a long-term partner. Even the most powerful ELN won’t help if your team doesn’t want to use it.

Why ease-of-use beats “extra” features

An intuitive ELN system:

• Reduces training time and ramp-up for new staff
• Lowers resistance from experienced scientists who are used to paper or spreadsheets
• Minimizes incomplete records and workarounds outside the system

Extra features can be useful, but not if they come at the cost of a cluttered interface and confusing workflows.

Red flags to watch for in demos

During demos or trials, watch for:

• Too many clicks to do simple tasks (e.g., start a new experiment, attach data, request a review)
• Confusing or inconsistent navigation between projects, experiments, and templates
• Weak or slow search, especially across older records
• Configuration screens that feel too complex for a typical lab admin

If it’s hard for a vendor’s expert to show you a clean, simple flow, it will be harder for your team to use that ELN system every day.

Questions to ask about training and support

Adoption depends heavily on what happens after go-live. Ask vendors:

• What onboarding and training options do you offer (live, on-demand, in-app help)?
• How do you support admins versus end users?
• What does ongoing support look like in practice—response times, channels, common issues?
• Do you have adoption playbooks or best practices for labs like ours?

 

How an Electronic Notebook Fits Into Your Data Ecosystem

An ELN should not become yet another silo. It needs to fit into the broader data ecosystem of your lab.

Integrations with instruments, LIMS, and data storage

List the systems your ELN system needs to connect with:

• Instruments generating key data files
• Existing LIMS or sample management tools
• File storage, SDMS, or analysis platforms

For each, ask:

• Does the ELN offer direct integrations, APIs, or standard import/export options?
• Can we automate data flows to avoid manual uploads where possible?
• How are large files, images, and complex data types handled?

The goal is to reduce double entry and manual manipulation, not add another step into already busy workflows.

IDs, naming conventions, and avoiding double entry

Consistent identifiers are critical. Make sure your ELN system can:

• Use or reference the same sample IDs, project IDs, or subject IDs as your LIMS or other systems
• Support naming conventions your team already understands
• Link experiments to samples, inventory, and results in a way that is easy to trace

If every system in your lab uses slightly different IDs, people end up reconciling everything manually and you lose many of the benefits of a modern ELN.

 

Bringing It All Together: A Simple Decision Framework

Once you’ve mapped goals and workflows and defined your requirements, you can create a simple decision framework for choosing an ELN system. Think of it as a short scorecard you can use across all ELN vendors.

Here are seven decision questions to include:

1. Does this ELN system clearly support our top 3–5 goals?
2. Can we model our real workflows in the system without heavy customization?
3. Is it easy for a new user to document an experiment and find old data without training?
4. Can it connect to the tools and systems we already rely on (instruments, LIMS, storage, analysis)?
5. Does it meet our minimum compliance and security needs today, with room to grow?
6. What does total cost of ownership look like over 3–5 years, not just year one?
7. Do we see a realistic path to adoption for all user types, not just power users?

You can translate these into a simple scorecard (for example, a 1–5 rating for each question). That way, you’re comparing ELN systems against your lab’s needs, not just against each other.

 

How LabKey’s ELN System Can Help

If you’re in the process of answering these questions, it can help to see how they play out with a real platform.

LabKey’s ELN software is designed to:

• Tie experimental records directly to samples, assays, and study data
• Support flexible, template-driven workflows without locking you into a single way of working
• Integrate ELN notebooks with broader data management capabilities across the LabKey platform

Because LabKey combines ELN functionality with sample management and scientific data management, you can track work from sample intake through analysis and reporting in a single environment, rather than stitching together multiple point solutions.

If you’re evaluating ELN systems and want to see how this framework looks in practice, you can [book a demo] to walk through your specific workflows and requirements.