U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights


Assessing Challenges and Benefits of an Online “Open Experiment”
Published: July 29, 2016
Posted: November 17, 2016

PNNL scientists explore a new model for research and data sharing.

The Science
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.

The Impact
Researchers in every field of science are being pushed—by funders, journals, governments, and their peers—to increase the transparency and reproducibility of their work. A key part of this effort is a move toward 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 used in this study is a way to help researchers achieve these goals and may serve as a model for others.

Summary
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.

Contacts (BER PM)
Daniel Stover and Jared DeForest
SC-23.1
Daniel.Stover@science.doe.gov, 301-903-0289; and Jared.DeForest@science.doe.gov, 301-903-1678

(PI Contact)
Ben Bond-Lamberty
Pacific Northwest National Laboratory
bondlamberty@pnnl.gov

Funding
This research was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Terrestrial Ecosystem Science program.

Publication
Bond-Lamberty, B., P. Smith, and V. Bailey. 2016. “Running an Open Experiment: Transparency and Reproducibility in Soil and Ecosystem Science," Environmental Research Letters 11(8), 084004. DOI: 10.1088/1748-9326/11/8/084004. (Reference link)

Related Links
https://github.com/bpbond/cpcrw_incubation

Topic Areas:

  • Research Area: Earth and Environment Systems Data Management
  • Research Area: Terrestrial Ecosystem Science

Division: SC-23.1 Climate and Environmental Sciences Division, BER

 

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