Advancing eDNA data: NatureMetrics transforms biodiversity research with Sapio Sciences' No/Low Code LIMS Platform

NatureMetrics is a global leader in providing nature data and intelligence. The company produces large-scale biodiversity data to support global sustainability and conservation efforts by utilizing state-of-the-art technology that can detect and identify environmental DNA (eDNA) left by organisms in water, sediment, soil, and air.

Scientist holding flask and working with laptop in lab

Image Credit: angellodeco/Shutterstock.com

To manage its unique and intricate next-generation sequencing (NGS) workflows, NatureMetrics needed more than patchwork spreadsheets. The company's main goal is to compile an extensive database of life on Earth that will assist humans in determining the best ways to protect it. Since implementing Sapio Sciences' cutting-edge, unified LIMS platform, the business has allowed NatureMetrics to:

  • Implement an out-of-the-box, end-to-end workflow for sample, material, and instrument management.
  • Track samples through a complex network of parallel and intersecting processes.
  • Simplify sample routing and decision-making by automating important quality control processes.

The customer

NatureMetrics, a global leader in nature intelligence technologies, offers a complete solution for impact reporting and nature monitoring. The company's eDNA-powered Nature Intelligence Platform converts species data at the site level into insightful management and monitoring of biodiversity and nature.

Businesses can manage their impacts and dependencies on biodiversity at scale thanks to the services provided by NatureMetrics. These services translate nature's complex nature into easily understood insights that help guide decisions about how operations affect sustainability, conservation, and the environment.

These services include a powerful impact monitoring and reporting platform, strategy development, and survey capabilities. The company's technology has facilitated biomonitoring in various global projects, such as mining operations in West Africa, conservation initiatives in the Amazon rainforest, and renewable energy infrastructure projects in the United Kingdom.

The challenge

Over time, NatureMetrics has amassed a network of linked databases and spreadsheets to oversee its diverse sequencing processes.

NatureMetrics said, “We developed somewhat clever methods of interlinking between spreadsheets and built dashboards to help manage processes.

However, as the company expanded, this soon proved restrictive, particularly when up to 40 NatureMetrics scientists required simultaneous access to data. Additionally, they noted that the spreadsheets lacked the data integrity required by NatureMetrics.

Furthermore, the inherent complexity of the current databases led to the creation of additional specialized satellite spreadsheets, which, although fit for their specific purposes, operated in isolation and were challenging to extract insights from automatically.

NatureMetrics explained, “We needed to mature our informatics environment to match the cutting-edge technology applied in other aspects of our business. Most of all, we needed a system that could support our complex workflows from start to finish and easily adapt as we made changes in our processes or added new types of experiments.”

The solution

In its initial search for a cutting-edge informatics solution, NatureMetrics examined 15 laboratory information management systems (LIMS). The NatureMetrics LIMS working group assessed five candidates, and three finalists were tested to determine which would be most appropriate for NatureMetrics' particular requirements.

NatureMetrics said, “We didn’t want to have to bend our processes to fit a LIMS. Rather, our goal was to find a system that could provide much of the functionality we required out of the box, with ways to perform easy configurations to the system to meet our needs without requiring massive amounts of coding.”

NatureMetrics chose the Sapio platform, which integrates a cloud-based scientific data management solution called Jarvis, an electronic laboratory notebook (ELN), and a LIMS. NatureMetrics said, “The openness and flexibility of the Sapio solution impressed us, and the low-code/no-code system has enabled us to define standard processes and, importantly, make changes as our needs and technology evolve.”

The Sapio system currently supports around 50 scientists who work in two labs in Canada and the United Kingdom.

Results/Benefits

NatureMetrics uses the Sapio platform to standardize its intricate NGS workflows and eliminate important data-management bottlenecks.

It was game-changing to find one out-of-the-box workflow that could cover our entire process from start to finish, including everything from indexing of samples to sequencing and delivering results to our clients,” said NatureMetrics.

For example, the Sapio system is set up to automatically assign samples to plates, meeting the different plating needs of the numerous assays and environments in the NatureMetrics product catalog. By automatically sorting samples as they enter the Sapio Process queue, the configuration has expedited the parallel processing of samples from various orders and projects.

The platform's capacity to handle pooled samples, which NatureMetrics uses to parallelize high-throughput sample sequencing, impressed scientists. As their samples and subsamples move through the NGS workflow, scientists can see a hierarchical, parent-child pedigree of them using the Sapio platform.

NatureMetrics made decisions about quality-control metrics and sensitivity more efficiently, thanks to the Sapio platform. Since NatureMetrics uses minuscule amounts of DNA extracted from environmental sources, a very high level of sensitivity is required. As a result, samples can become contaminated by people and more prevalent species, like domestic animals and livestock. Monitoring and containing possible contaminants is made easier by the Sapio platform, which tracks all related supplies, reagents, and equipment used in the experiments.

Before NatureMetrics deployed the Sapio platform, scientists held regular meetings to review experimental metrics and decide which samples should be rerun if quality control failed. The Sapio platform can automatically make a range of quality-control decisions by applying a set of preconfigured rules. These rules can be used to reject samples that do not meet predetermined criteria or reroute samples back through sequencing when thresholds are reached.

This hard set of rigorous quality control rules is enabling us to eliminate these meetings so that we can better focus resources on processing samples through the lab,” said NatureMetrics.

During the Sapio platform implementation process, NatureMetrics discovered several important insights.

  • Having thorough records of the requirements and current procedures made it possible for the business to deploy the Sapio platform swiftly.
  • Acceptance criteria were specified at each stage of implementation, and everyone remained in alignment through kick-off meetings with Sapio.
  • Testing was essential. “We tried to break the system during the UAT phase to know exactly how the system would react to different scenarios,” said NatureMetrics.
  • NatureMetrics ran the Sapio platform concurrently with the organization's previous systems to go live with the system. This helped with training and allowed NatureMetrics to identify any lingering bugs and issues during the rollout. 

NatureMetrics plans to integrate other features currently handled by different platforms, such as tools for monitoring inventory levels and equipment upkeep. Dashboards are also being used for various scientific tasks. Long term, the company intends to directly integrate the Sapio platform with other business systems, such as NatureMetrics's data warehouse and ERP and instrument software.

Last updated: May 1, 2024 at 5:25 AM

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