According to Vinay Prasad, an oncologist and one of the authors of the Mayo Clinic Proceedings paper, medicine is quick to adopt practices based on shaky evidence but slow to drop them once they’ve been blown up by solid proof. As a young doctor, Prasad had an experience that left him determined to banish ineffective procedures. He was the medical resident on a team caring for a middle-aged woman with stable chest pain. She underwent a stent procedure and suffered a stroke, resulting in brain damage. Prasad, now at the Oregon Health and Sciences University, still winces slightly when he talks about it. University of Chicago professor and physician Adam Cifu had a similar experience. Cifu had spent several years convincing newly postmenopausal patients to go on hormone therapy for heart health—a treatment that at the millennium accounted for 90 million annual prescriptions—only to then see a well-designed trial show no heart benefit and perhaps even a risk of harm. "I had to basically run back all those decisions with women," he says. "And, boy, that really sticks with you, when you have patients saying, 'But I thought you said this was the right thing.'" So he and Prasad coauthored a 2015 book, Ending Medical Reversal, a call to raise the evidence bar for adopting new medical standards. "We have a culture where we reward discovery; we don’t reward replication," Prasad says, referring to the process of retesting initial scientific findings to make sure they’re valid.
At AAAS 2017, a pair of panel discussions addressed the reproducibility crisis in science, particularly biomedical science, and suggested that it is manageable, provided stakeholders continue to demonstrate a commitment to quality. One panel, led by Leonard P. Freedman, Ph.D., president of Global Biological Standards Institute (GBSI), was comprehensive. It prescribed a range of initiatives.
As a principal investigator, how do you run your lab for reproducibility? I submit the following action areas: commitment, transparency and open science, onboarding, collaboration, community and leadership. Make a public commitment to reproducible research—what this means for you could differ from others, but an essential core is common to all. Transparency is an essential value, and embracing open science is the best route to realize it. Onboarding every lab member with a deliberate group “syllabus” for reproducibility sets the expectations high. What is your list of must-read literature on reproducible research? I can share mine with you: my lab members helped to make it. For collaborating efficiently and building community, we take inspiration from the open-source world. We adopt its technology platforms to work on software and to communicate, openly and collaboratively. Key to the open-source culture is to give credit—give lots of credit for every contribution: code, documentation, tests, issue reports! The tools and methods require training, but running a lab for reproducibility is your decision. Start here–>commitment.
One year after the Global Biological Standards Institute (GBSI) issued its Reproducibility2020 challenge and action plan for the biomedical research community, the organization reports encouraging progress toward the goal to significantly improve the quality of preclinical biological research by year 2020. "Reproducibility2020 Report: Progress and Priorities," posted today on bioRxiv, identifies action and impact that has been achieved by the life science research community and outlines priorities going forward. The report is the first comprehensive review of the steps being taken to improve reproducibility since the issue became more widely known in 2012.
We are currently in one of the most exciting times for science and engineering as we witness unprecedented growth computational and experimental capabilities to generate new data and models. To facilitate data and model sharing, and to enhance reproducibility and rigor in biomechanics research, the Journal of Biomechanics has introduced a number of tools for Content Innovation to allow presentation, sharing, and archiving of methods, models, and data in our articles. The tools include an Interactive Plot Viewer, 3D Geometric Shape and Model Viewer, Virtual Microscope, Interactive MATLAB Figure Viewer, and Audioslides. Authors are highly encouraged to make use of these in upcoming journal submissions.
Reproducibility is an important part of scientific research and studies published in speech and language research usually make some attempt at ensuring that the work reported could be reproduced by other researchers. This paper looks at the current practice in the field relating to the citation and availability of both data and software methods. It is common to use widely available shared datasets in this field which helps to ensure that studies can be reproduced; however a brief survey of recent papers shows a wide range of styles of citation of data only some of which clearly identify the exact data used in the study. Similarly, practices in describing and sharing software artefacts vary considerably from detailed descriptions of algorithms to linked repositories. The Alveo Virtual Laboratory is a web based platform to support research based on collections of text, speech and video. Alveo provides a central repository for language data and provides a set of services for discovery and analysis of data. We argue that some of the features of the Alveo platform may make it easier for researchers to share their data more precisely and cite the exact software tools used to develop published results. Alveo makes use of ideas developed in other areas of science and we discuss these and how they can be applied to speech and language research.