The Traps and Challenges of LIMS and ELN Selection

by | 13. 11. 2023 | Laboratory digitalization

Reading Time: 9 minutes

LIMS (Laboratory Information Management System) and ELN (Electronic Laboratory Notebook) offer several benefits that can enhance laboratory operations and research activities. But when choosing the right LIMS or ELN solution for your laboratory, you will soon find yourself baffled by how many vendors there are on the market.

The primary reason for the abundance of LIMS and ELN solutions is the diversity of laboratory needs. Each laboratory has unique requirements based on its industry, the nature of the research or analysis they perform, its lab size, the level of automation required, workflows, and the type of data and information generated and stored.

Additionally, regulations and compliance requirements vary across industries and countries, further contributing to the diversity of laboratory needs. As a result, there are hundreds of LIMS and ELN solutions on the market.

The potential for selecting an unsuitable LIMS or ELN solution for your lab is considerable. Failing to approach the process with due diligence, inadequate knowledge, or time constraints can result in an incompatible choice. Implementing new software is challenging, and transitioning from one system to another can prove even more difficult, demanding significant effort. Recognizing the potential pitfalls and equipping yourself with the necessary knowledge to navigate the selection process successfully is crucial.

To help you on this journey, we collected some of the most common challenges and pitfalls in the LIMS or ELN selection process.

Main challenges in choosing the right LIMS or ELN software

1. Lack of laboratory process assessment

Process assessment is tightly connected to laboratory digitalization as you need to understand your processes before deciding which LIMS or ELN solution to implement in your laboratory. Furthermore, by taking this step, you will not only acquire knowledge about which digital solution to choose, but you will also gain a deeper understanding of your laboratory’s operations. Identifying areas that may be hindering productivity, efficiency, quality, and safety will become possible. Armed with this knowledge, you can optimize your laboratory processes and approach the implementation of new software for life sciences or other industry with increased ease and confidence.

To assess your laboratory effectively, it is advisable to create a process map. This involves identifying all relevant processes and actively involving the people who carry them out, as they possess valuable insights into the actual workflow.

Documenting extensive information about each process and its interconnections is crucial. It is essential to determine the starting and ending points of each process and understand their sequential flow. Next, you should draw a process map with appropriate symbols for the start/end of the process, activities, flow, decisions, and inputs/outputs. In the end, this process mapping exercise will enable you to pinpoint all bottlenecks and limitations within your processes. Fortunately, many of these issues can be resolved through the adoption of digitalization solutions in biotech companies like LIMS and ELN tools.

You can read more about how to assess your processes and draw a process map in our blog post Laboratory Processes Mapping.

2. Poor definition of laboratory requirements

To understand what LIMS and ELN solution would best fit your laboratory or organization, you first thing must first clearly define your specific requirements that align with your laboratory’s needs and workflows. Following the assessment of your laboratory, consider the following questions:

  • What type of data does your laboratory generate? Experimental data, sample information, metadata? What kind of data management or do you need?
  • What level of security or version control do you require to protect? Do you need to ensure compliance with regulatory standards? Is your laboratory environment subject to any regulations, such as GxP, FDA 21 CFR Part 11, EU GMP Annex 11, and ISO 17025?
  • Which areas in your laboratory workflows can benefit from automation? Would main functions like workflow management, inventory management, electronic signatures, data analysis, task assignment, or notifications enhance the efficiency of your processes?
  • Do you require sample tracking and management?
  • Is there a need for integration with laboratory instruments, devices, and other systems such as ERP (Enterprise Resource Planning) or LIMS-to-LIMS integration for data exchange with external laboratories or collaborators?
  • What kind of collaboration needs can you identify between your team members for easier collaboration and teamwork? Consider features like document sharing, commenting, and version control.
  • How many users will use the solution, and what are the needs of their different roles?

There are just some of the requirements you should consider, and they can differ according to the type or specifics of your laboratory or organization. If you don’t have the answer to these questions, there is a high possibility that your user requirements will be poorly defined and the selection of your LIMS or ELN solution won’t be a good fit.

3. Lack of clear vision

Just as important as an understanding of current work processes and requirements in your laboratory is the understanding of the future of your lab. One common mistake in the LIMS or ELN solution selection process is the lack of long-term vision of laboratory operations. Consider the future growth and scalability of your laboratory. Determine if the solution can accommodate increasing data volumes, new experiments, additional users, and changing workflows.

What do you anticipate doing in the future? Will you focus solely on a specific type of testing, or are you planning to expand into other types of analytical work? Are you planning to expand soon? Do you plan to open new facilities? These and other related questions will help shape your long-term vision and guide the selection process. Will the chosen solution be able to accommodate these growth factors?

Scalability becomes a crucial factor, as you want a system that can seamlessly adapt to the changing demands of your laboratory. Consider whether the solution offers flexibility, customization options, and the ability to integrate with other systems or instruments.

Additionally, think about the potential challenges and opportunities that may arise in your industry. Stay informed about emerging technologies, regulatory changes, and industry trends that could impact your lab.

By considering your future aspirations and requirements, you can make an informed decision during the selection process. This forward-thinking approach ensures that the chosen LIMS (laboratory inventory management system) or ELN solution will not only meet your current needs but also position your laboratory for success in the years to come.

4. No prioritization of requirements

There is a lot of offer on the LIMS and ELN market, but it is very likely that you won’t find the solution that would perfectly fit all your challenges and requirements. While some vendors aim to create a universal solution, others may concentrate on specific areas or purposes.

There might be customized solutions, but that might not be an option if your budget is limited. Therefore it is important to focus on the priorities. What are the biggest gaps in your processes you are looking to address? Prioritize your challenges and requirements and start from there. You should begin with workflow, features, and data management requirements and continue with more specific requirements like integrations, regulatory, security, system, and other requirements.

Once you have identified solutions that align with your prioritized requirements, it’s essential to address other non-prioritized requirements as well. While these may not be critical, they can still add value to your laboratory’s operations and contribute to a more comprehensive solution.

Create a list of all potential solutions that meet the prioritized requirements and within these options, look for those that not only cover the highest-priority needs but also address most of your non-prioritized requirements. Ensuring that the chosen solution covers a significant portion of your additional features will guarantee that it aligns well with your laboratory’s overall needs and maximizes the benefits it can provide.

5. Hidden costs in LIMS or ELN pricing

When pricing a laboratory informatics solution, you have two main options: a one-time license fee or a subscription rate for cloud-hosted software (SaaS). The one-time license fee may be preferred if you have your own IT staff. Subscription costs are typically due at signing, with some vendors requiring upfront payment for three months or the first year. Additionally, price tags can be based on the number of users.

The problem arises when you don’t thoroughly examine the additional costs of LIMS or ELN solutions, as they are often not initially disclosed during the selection process. Many solutions have varying pricing models that encompass upfront costs, subscription fees, maintenance fees, and additional expenses for customization, implementation, or integration.

Evaluating the total cost of ownership can be a complex task, particularly without prior experience. It is not uncommon for the actual post-implementation costs to exceed the initially defined budget. Careful consideration and assessment of all potential costs are necessary to avoid any unexpected financial implications.

6. User resistance to new LIMS or ELN solution

When selecting a LIMS or ELN solution, it can be challenging to predict upfront whether the lab personnel will embrace the new life sciences software. However, it is crucial to consider and address possible user resistance during the selection process. One of the key mistakes is when the decision about the LIMS solution is made solely by laboratory management or individuals who are not directly involved in laboratory work. To mitigate this, effective communication with laboratory personnel and seeking their opinions is essential.

To ensure a smooth transition and user adoption, it is important to assess the user interface and ease of use of the chosen solution. This evaluation should be conducted by individuals with hands-on experience in laboratory work who understand the specific needs of different user roles. The best solution should offer an intuitive interface, customization options, and efficient data entry and retrieval capabilities to support the diverse requirements of laboratory personnel.

Additionally, evaluating the level of support, training, and documentation the vendor provides is crucial. Consider whether the vendor offers timely technical support, comprehensive training resources, and user guides to facilitate the implementation and provide ongoing assistance.

If feasible, requesting a demo presentation and free trial period can be beneficial. This allows you to test the solution with your team, gaining firsthand experience of how it would function in the long run. This trial period provides insights into the solution’s usability, functionality, and compatibility within your laboratory environment.

7. Mitigating LIMS or ELN vendor bias

One of the significant and most deceitful challenges in selecting LIMS (laboratory information management system) or ELN (electronic lab notebook) solution lies in the potential bias of vendors. While vendors may portray their solutions as the perfect fit for your needs, it is crucial to recognize the possibility of a lack of a balanced perspective regarding the drawbacks and limitations of their systems. Vendors’ opinions may be biased in favor of their own solution, potentially obscuring an objective view of the product’s true capabilities and limitations.

While evaluating vendors, consider seeking objective information from independent sources and user reviews to comprehensively understand the system’s strengths and weaknesses. Engaging in thorough discussions with vendors, posing critical questions, and requesting detailed demonstrations can help uncover potential limitations that might not be initially apparent. Furthermore, ask them for references from other labs they’ve worked with.

Acknowledging that certain issues may only arise after the system has been implemented is crucial. These challenges can include system flexibility limitations, configuration difficulties, integration problems with existing infrastructure, and unforeseen additional costs.

Possessing the knowledge and skills required to engage with vendors is essential, ensuring thoughtful and critical communication while carefully evaluating their responses. To navigate the complexities and mitigate vendor bias, enlisting the assistance of a professional and experienced consultant can be highly beneficial.

An unbiased consultant with extensive research activities skills brings valuable expertise and industry knowledge to the selection process, offering an impartial perspective. It can advocate for your laboratory’s best interests, providing guidance and support throughout the selection process and helping you make an informed decision that aligns with your unique requirements and ensures the long-term success of your laboratory informatics solution.

The danger of underestimating the Scope in the LIMS and ELN Selection Process

While being aware of the risks mentioned earlier can significantly assist in choosing the right LIMS or ELN system for your lab, there is yet another challenge to consider – the significance of the selection process itself. Underestimating the selection process can lead to unforeseen complications.

To make a well-informed decision and find the best solution, allocating a substantial amount of time is crucial. The process involves tasks such as assessing the laboratory processes, writing the User Requirements Specification (URS), thoroughly evaluating various solutions, and engaging in extensive communication with vendors. Rushing the process and choosing a solution hastily can result in numerous issues that arise later.

Choosing a solution without adequate time investment may lead to unexpected costs emerging, hidden expenses becoming apparent, and subsequent problems occurring. The system may incur significant charges, and valuable time will be consumed in resolving and optimizing it. Ultimately, you may find yourself needing to replace the system soon after implementation, creating a cycle of inefficiency and wasted resources.

In the table below, we provide an estimation of the time required for key steps in the selection process. These estimates serve as a rough approximation, with more complex solutions demanding even more time. Therefore, if you are contemplating handling the task independently, it is crucial to recognize that a proper selection process can take a minimum of 380 hours.


Table 2: Steps and time needed to choose the right LIMS or ELN solution

StepEstimated Time Required
Assessing your lab45 hours
Defining requirements80 hours
Writing URS20 hours
Reviewing solutions85 hours
Evaluating solutions40 hours
Communication with vendors80 hours
Decision making and contract negotiations30 hours
TOTAL380 hours


The optimal way to approach LIMS and ELN selection

Considered by some as an additional expense, hiring a third-party consultant actually emerges as a cost-effective solution for both short and long-term objectives. Expertise, time savings, and cost efficiency are the key reasons behind this realization.

Firstly, consultants possess extensive expertise in laboratory processes, workflows, data management, and regulatory compliance requirements. Their deep understanding enables them to identify your lab’s specific needs and recommend the most suitable LIMS or ELN solution. This expertise helps avoid costly mistakes and ensures that the provided solution precisely aligns with your requirements.

Secondly, consultants are well-versed in the technology behind LIMS and ELN systems. Their proficiency allows them to efficiently navigate the vast array of options and identify the right solution for your lab. This saves you significant time and effort researching and evaluating various vendors and their offerings.

Lastly, consultants often maintain comprehensive databases of pre-selected and evaluated vendors. Leveraging their existing knowledge and resources, they can efficiently match your requirements with suitable vendors, streamlining the selection process. This results in cost savings by reducing the time spent on vendor evaluation, negotiation, and potential implementation setbacks.

While the upfront cost of consulting services may seem substantial, the long-term benefits and savings outweigh the initial expenses. By harnessing their expertise, you can avoid costly mistakes, minimize implementation challenges, and ensure the selected LIMS or ELN solution optimally serves your lab’s needs.

BioSistemika provides vendor-independent consulting services with valuable expertise and experience in the field of LIMS and ELN selection. Our interdisciplinary team with diverse health and life science backgrounds can provide unbiased guidance tailored to your specific requirements.

Contact us to learn how we can assist you in finding the optimal LIMS or ELN solution for your laboratory.

You can read more about why to hire a consultant in our blog article Benefits of Hiring a Digitalization Expert.

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