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Legacy Software Imposes Significant Challenges on NGS Clinical Diagnostic Labs & Evolving LIMS

Laboratory and technical leads face a number of complex challenges when changes to an existing process are required. Whether they want to add new assays, tests or products, take advantage of new equipment, or scale throughput, these challenges can lead them to wonder: Are my legacy systems adequate? Can or should these legacy systems be further customized? Should we consider a wholesale system replacement? What’s the most cost-effective approach to meeting our business needs?

In part, these questions arise because existing laboratory information management systems (LIMS) and laboratory software solutions are often not built in a way that makes them easily extensible or scalable. But there are other issues as well.

Existing Legacy Solutions Often Hinder Usability & Efficiency

Labs that rely on legacy systems may not be aware of the usability limitations of their existing systems. But for users, older software can mean performing tasks less effectively, efficiently, and safely, so that they’re not making the best use of their valuable time. Modern software, on the other hand, offers a better user experience and more likelihood that the business will reach its goals and meet regulatory requirements.

Legacy systems can be less stable, require significantly more maintenance, and present a higher risk to the business. Modern software solutions provide labs with a strong foundation so that they are easier to scale, maintain, and grow.

Not Built for Change or Scalability

Many labs are still using either a solution that has been developed internally or a commercial-off-the-shelf LIMS implementation that has not been built for change. In these systems, workflows might be hard-coded instead of managed through a configuration interface. Even for labs that have software developers on hand, hard-coded workflows are difficult and time-consuming to change, especially when compatibility with historical data must be maintained and all changes validated.

Since processes are bound to change and grow, a LIMS that relies on hard-coded workflows can quickly become a drag on process improvements, particularly in the case of high complexity labs. A solution that enables changes to be made through a user interface significantly improves a lab’s ability to keep up with evolving processes and to scale effectively.

Version control can also be an issue for legacy systems. At many labs, deploying new versions of the LIMS is a manual and risky process with numerous opportunities for error. Modern software adheres to strict version control so that users always know which specific software version they are using. If necessary, they can roll back to previous versions because all the changes have been tracked and managed.

The True Cost of Existing Systems Is Not Well Understood

Labs often significantly underestimate the cost of their software systems. The true cost includes:

  • Original cost of implementing the system. This includes not just the actual development cost but also the cost of identifying requirements, and performing testing and validation.
  • Ongoing cost of running the system. This includes the degree of manual intervention required, the cost of training and support, and the cost of system inefficiencies that result from poor usability.
  • Ongoing cost of running the system. Cost to evolve the system and update workflows and to work around the limitations of the system.
  • Cost of personnel. Frequently personnel costs are not allocated to the system but are hidden in the running costs of the organization.

Over the medium to long term, a modern software solution can offer significant cost savings.

Key Personnel Are Not Easy to Replace

Labs frequently underestimate the likelihood of losing personnel who have a comprehensive understanding of the legacy system, whether it’s developed in house or a commercial-off-the-shelf solution that’s heavily customized. Imagine losing key personnel when they take a leave of absence or return to their primary position. Or worse, losing the entire development team at a critical turning point. It’s been known to happen, and can be particularly devastating for businesses using multiple interrelated, highly customized commercial-off-the-shelf systems.

Organizations that have internal systems built by individuals over an extended period of time are in a particularly precarious position. These systems can be difficult for a new person or group to take over. Often it is not clear what the current state of the system is, where the source code is kept, or what deployment-specific configuration needs to be performed. At one company, it took nearly nine months for the new team to be able to reliably build and deploy the existing production system directly from source—an expensive lesson.

Losing key staff results in not just a loss of knowledge, but also a financial hit when it comes to training their replacements. It’s essential for labs to think about the long-term reality of staff changes when they plan to evolve a LIMS implementation. Apart from the cost, it’s not always easy to replace staff either. The market for experienced LIMS engineers and software developers is currently extremely competitive so internal development teams can struggle to compete with new startups and product companies.

Personnel May Lack Specialized Software Expertise

Even for labs lucky enough not to experience high turnover, a lack of specialized software expertise among key personnel can be a tremendous impediment. And yet, this is something we commonly see. Often LIMS implementations are completed by people who have extensive laboratory and science domain experience or specific bioinformatics experience, but lack knowledge in software engineering principles and best practices.

Specifically, labs can experience the following challenges:

  • Lack of experience in scaling. Some personnel are not aware of or have limited experience with the methodologies and patterns of developing large scale software that must be maintained over time. This can result in developing software that exactly meets the requirements at the time but is difficult or impossible to extend for future needs.
  • Lack of easily repeatable processes, resulting in delays and missed deadlines. Personnel who employ modern software development practices place a high value on being able to quickly and repeatedly deploy systems, both from scratch and for upgrades.
  • Lack of sound software design and architecture, resulting in complex software structures that cannot be generalized for the use of more than one group within the organization. Purpose-built legacy systems, which might use mutually incompatible data models, are often difficult to build, upgrade, and integrate, and can get in the way of achieving the core purpose of the business.

If you’re thinking about upgrading or replacing your LIMS, I recommend carefully considering each of these issues before you proceed.

In my next post, we’ll look at how you can future-proof your NGS Clinical Diagnostic lab so that you can change workflows, meet new regulatory requirements, or scale throughput quickly and easily.

Mark Swinkles is co-founder and CTO of Semaphore Solutions. With over thirty years of experience as a software professional, Mark leads the technical team who provides Semaphore's clients successful NGS LIMS implementations across the globe.