Berkeley Lab Scientist Joins Fellow Scholars Against Withholding Computing Source Codes in Publishing Scientific Results
The advancement of science and technology depends upon the publication and open exchange of knowledge and materials, a backbone that has always been obligatory with regards to publicly funded research. In recent years, however, the ever-increasing reliance on computing has created scientific “black boxes” in the form of computer source code that is critical to understanding and evaluating the research but is often withheld information. In a Public Forum essay in the journal Science, a distinguished group of scholars including Paul Adams of the Lawrence Berkeley National Laboratory (Berkeley Lab) has put forth recommendations for solving this growing problem.
In their Public Forum essay, Adams and his co-authors argue that these source code black boxes are creating far-reaching problems for understanding and reproducing new scientific research findings. The withholding of source codes is also contributing to the perception of a “credibility crisis” for computation research.
“Source code is the human readable form of a programming language and contains the complete set of instructions for how a computer processes input data. In the absence of source code, the inner workings of a program cannot be examined, adapted or modified,” state the authors. “Source code withholding causes duplication of efforts by preventing the sharing and reuse of validated computer code, and is incompatible with the stated goals of science funding agencies and policy advisory bodies.”
The Public Forum essay is titled “Shining Light into Black Boxes.” Co-authoring it with Adams were Andrew Morin and Piotr Sliz of Harvard Medical School, Jennifer Urban of the University of California (UC) Berkeley Law School, Ian Foster of the Argonne National Laboratory, Andrej Sali of UC San Francisco, and David Baker of the University of Washington. Adams, in addition to his appointment with Berkeley Lab’s Physical Biosciences Division, is also a UC Berkeley Bioengineering professor and leads the Technologies Division of the U.S. Department of Energy’s Joint BioEnergy Institute (JBEI).
In publicly funded research, the creation and dissemination of new tools, techniques and methods requires detailed publication and disclosure of information necessary to satisfy peer review, experimental reproduction, and the ability to build upon another’s work. However, as Adams and his co-authors note, “Disclosure practices among scientist programmers often do not meet these standards.”
Protectionism is only one of a number of potential reasons for the computer source code disclosure disparity, but perhaps the most significant factor, the authors say, is “the absence of a universal disclosure requirement by the gatekeepers of scientific publishing.” Out of the 20 most cited scientific journals, only three, including Science, require that computer source codes be made available upon publishing.
“This stands in stark contrast to near-universal agreement among the 20 on policies regarding availability of data and other enabling materials,” the authors state.
To correct the problem, Adams and his co-authors call upon publicly funded research institutions and universities to remove organizational impediments to open source software licensing of computer code. They also ask public funding and policy-setting agencies to state a strong preference for open dissemination, sharing, and publication of scientist-created software and source code. Finally, they urge scientific journal publishers to require, as a condition of publication, that researchers make available new computer source code generated in the course of the research and necessary to reproduce the published research findings.
“If enacted, we expect these recommendations to yield substantial benefits including improved code quality, reduced errors, increased reproducibility, and greater efficiency through code reuse and sharing,” the authors state.
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Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. For more, visit www.lbl.gov.