Stewart Lowndes, Julia; Best, Benjamin D.; Scarborough, Courtney E.; Afflerbach, Jamie; Frazier, Melanie; O'Hara, Casey; Jiang, Ning; Halpern, Benjamin S. 2017. Our path to better science in less time using open data science tools. Nature Ecology & Evolution. (Abstract) (Online version)
Reproducibility has long been a tenet of science but has been challenging to achieveâ€”we learned this the hard way when our old approaches proved inadequate to efficiently reproduce our own work. Here we describe how several free software tools have fundamentally upgraded our approach to collaborative research, making our entire workflow more transparent and streamlined. By describing specific tools and how we incrementally began using them for the Ocean Health Index project, we hope to encourage others in the scientific community to do the sameâ€”so we can all produce better science in less time. Science, now more than ever, demands reproducibility, collaboration and effective communication to strengthen public trust and effectively inform policy. Recent high-profile difficulties in reproducing and repeating scientific studies have put the spotlight on psychology and cancer biology, but it is widely acknowledged that reproducibility challenges persist across scientific disciplines. Environmental scientists face potentially unique challenges in achieving goals of transparency and reproducibility because they rely on vast amounts of data spanning natural, economic and social sciences that create semantic and synthesis issues exceeding those for most other disciplines. Furthermore, proposed environmental solutions can be complex, controversial and resource intensive, increasing the need for scientists to work transparently and efficiently with data to foster understanding and trust. Environmental scientists are expected to work effectively with ever-increasing quantities of highly heterogeneous data even though they are seldom formally trained to do so. This was recently highlighted by a survey of 704 US National Science Foundation principal investigators in the biological sciences, which found training in data skills to be the largest unmet need15. Without training, scientists tend to develop their own bespoke workarounds to keep pace, but with this comes wasted time struggling to create their own conventions for managing, wrangling and versioning data. If done haphazardly or without a clear protocol, these efforts are likely to result in work that is not reproducibleâ€”by the scientist's own â€˜future selfâ€™ or by anyone else. As a team of environmental scientists tasked with reproducing our own science annually, we experienced this struggle first-hand. When we began our project, we worked with data in the same way as we always had, taking extra care to make our methods reproducible for planned future re-use. But when we began to reproduce our workflow a second time and repeat our methods with updated data, we found our approaches to reproducibility were insufficient. However, by borrowing philosophies, tools, and workflows primarily created for software development, we have been able to dramatically improve the ability for ourselves and others to reproduce our science, while also reducing the time involved to do so: the result is better science in less time (Fig. 1). Here we share a tangible narrative of our transformation to better science in less timeâ€”meaning more transparent, reproducible, collaborative and openly shared and communicated scienceâ€”with an aim of inspiring others. Our story is only one potential path because there are many ways to upgrade scientific practicesâ€”whether collaborating only with your â€˜future selfâ€™ or as a teamâ€”and they depend on the shared commitment of individuals, institutions and publishers. We do not review the important, ongoing work regarding data management architecture and archiving, workflows, sharing and publishing data and code or how to tackle reproducibility and openness in science. Instead, we focus on our experience, because it required changing the way we had always worked, which was extraordinarily intimidating. We give concrete examples of how we use tools and practices from data science, the discipline of turning raw data into understanding. It was out of necessity that we began to engage in data science, which we did incrementally by introducing new tools, learning new skills and creating deliberate workflowsâ€”all while maintaining annual deadlines. Through our work with academics, governments and non-profit groups around the world, we have seen that the need to improve practices is common if not ubiquitous. In this narrative we describe specific software tools, why we use them, how we use them in our workflow, and how we work openly as a collaborative team. In doing so we underscore two key lessons we learned that we hope encourage others to incorporate these practices into their own research. The first is that powerful tools exist and are freely available to use; the barriers to entry seem to be exposure to relevant tools and building confidence using them. The second is that engagement may best be approached as an evolution rather than as a revolution that may never come.