September 13, 2016
Assessing the Challenges and Benefits of an Online “Open Experiment”
PNNL scientists explore a new model for research and data sharing.
Scientists conducted an “open experiment” in which every aspect of a laboratory experiment was documented online and in real time. This model pushed the researchers to write higher-quality analysis code, shortened the time required to do so, enabled them to quickly identify problems, and resulted in a stronger publication.
Researchers in every field of science are being pushed—by funders, journals, governments, and their peers—to increase transparency and reproducibility of their work. A key part of this effort is a move towards open data as a way to fight post-publication data loss, improve data and code quality, enable powerful meta- and cross-disciplinary analyses, and increase public trust in and the efficiency of,publicly funded research. The approach described used in this study is a way to help researchers achieve these goals and may serve as a model for interested researchers.
In early 2015, Department of Energy scientists at Pacific Northwest National Laboratory planned a laboratory incubation experiment to characterize the chemical and biological properties of sub-Arctic, active-layer soils subjected to changes in temperature and moisture. This experiment required (1) a multidisciplinary team that was not located in one time zone; (2) integration of various data; (3) rapid performance of quality control and diagnostics, so that if instrument problems arose the team would lose only the minimum amount of time and data; and (4) tight integration of data, statistical analyses, and manuscript results. The team designed a data processing and analytical system written in an open-source and widely used language for statistical computing and graphics, and placed it in a publicly available “repository” that stored all code and data, making them available in real time. Using an automated analytical pipeline in an open repository provided significant advantages for the project, but the costs of such an approach and investments required should also be considered.
Pacific Northwest National Laboratory
U.S. Department of Energy, Biological and Environmental Research (SC-33)
Environmental System Science
This research was supported by the Terrestrial Ecosystem Science program of the Office of Biological and Environmental Research within the U.S. Department of Energy Office of Science.
Bond-Lamberty, B., P. Smith, and V. Bailey. "Running an open experiment: Transparency and reproducibility in soil and ecosystem science." Environmental Research Letters 11 084004 (2016). https://doi.org/10.1088/1748-9326/11/8/084004.