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Building open-access tools to monitor pharmaceuticals impact in the aquatic environments

This case study is by Dr Kishore Kumar Jagadeesan, a Postdoctoral Research Associate specialising in wastewater-based epidemiology and environmental monitoring.

Diagram of an open-source tool to help monitor levels of pharmaceutical pollution in waterways
Diagram of an open-source tool to help monitor levels of pharmaceutical pollution in waterways

Summary

We created PERK (Predicting Environmental Concentration and Risk), an open-source R package with an R/Shiny application, to predict and visualize pharmaceutical pollution in waterways, sharing it freely with researchers, policymakers, and environmentalists.

By making PERK open-access, we ensured transparency, reproducibility, and global access, allowing users to adapt it for local environmental challenges. Inspired by rapid advances in environmental monitoring, we aimed to empower scientists and communities to tackle pharmaceutical pollution together.

Our work at the University of Bath’s Centre of Excellence in Water-Based Early-Warning Systems for Health protection shows how open tools can drive collaboration and trust in research, enabling anyone to monitor pharmaceuticals in rivers and assess risks to ecosystems and health.

Context

Our PERK project aimed to predict levels of active pharmaceutical ingredients (APIs) in waterways, addressing how medicines pollute rivers and threaten ecosystems and public health. We wanted a user-friendly tool to help researchers and policymakers monitor these risks. Using data from the UK’s National Health Service, wastewater treatment studies, and environmental models, we built an R/Shiny application that combines API prescription, human metabolism, and river dilution data to create predictive maps and charts.

We chose open-source software development to make PERK free for all, inspired by the need for transparent, and reproducible science. This approach let global researchers verify our methods, adapt PERK for their rivers, and build on our work, aligning with our goal to maximize impact in solving a critical environmental problem.

Reflections

  • Releasing PERK as open-source software presented challenges. We initially struggled to ensure the tool was accessible to non-experts while maintaining robust functionality.
  • Documenting code for public use was time-consuming, raising concerns about publication delays.
  • Additionally, we had to balance transparency with the sensitivity of certain datasets, such as prescription data. We addressed these by adopting clear documentation standards and leveraging GitHub for code sharing and usability.
  • Lessons learned include planning for open access from the project’s start, balancing transparency with data privacy, and valuing community input for refining tools.

Take-home Message

Releasing PERK as open-source empowered global collaboration in tracking pharmaceutical pollution, proving that shared tools drive impactful, transparent environmental solutions.

About the Author

Dr Kishore Kumar Jagadeesan is a Postdoctoral Research Associate specialising in wastewater-based epidemiology and environmental monitoring. He focuses on developing open, reproducible analytical workflows in R to support public health and environmental risk assessment. His collaborators, John Bagnall (Wessex Water), Megan Robertson (Wessex Water), Ruth Barden (Wessex Water), and Professor Barbara Kasprzyk-Hordern (University of Bath), provided critical expertise in environmental science and project guidance.

Links

Find out more about Open Research at the University of Bath

Open Research at the University of Bath