Posts about reproducible paper (old posts, page 16)

Reproducibility and Validity of a Food Frequency Questionnaire Designed to Assess Diet in Children Aged 4-5 Years

The food frequency questionnaire (FFQ) is the most efficient and cost-effective method to investigate the relationship between usual diet and disease in epidemiologic studies. Although FFQs have been validated in many adult populations worldwide, the number of valid FFQ in preschool children is very scarce. The aim of this study was to evaluate the reproducibility and validity of a semi-quantitative FFQ designed for children aged 4 to 5 years.

Reproducible research: Stripe’s approach to data science

When people talk about their data infrastructure, they tend to focus on the technologies: Hadoop, Scalding, Impala, and the like. However, we’ve found that just as important as the technologies themselves are the principles that guide their use. We’d like to share our experience with one such principle that we’ve found particularly useful: reproducibility. We’ll talk about our motivation for focusing on reproducibility, how we’re using Jupyter Notebooks as our core tool, and the workflow we’ve developed around Jupyter to operationalize our approach.

Reproducibility and research misconduct: time for radical reform

We know now that much health and medical research which is published in peer-reviewed journals is wrong,[1] and consequently much is unable to be replicated.[2-4] This is due in part to poor research practice, biases in publication, and simply a pressure to publish in order to ‘survive’. Cognitive biases that unreasonably wed to our hypotheses and results are to blame.[5] Strongly embedded in our culture of health and medical research is the natural selection of poor science practice driven by the dependence for survival on high rates of publication in academic life. It is a classic form of cultural evolution along Darwinian lines.[6, 7] Do not think that even publications in the most illustrious medical journal are immune from these problems: the COMPare project[8] reveals that more than 85% of large randomised controlled trials deviate seriously from their plan when the trial was registered prior to its start. An average of more than five new outcome measures was secretly added to the publication and a similar number of nominated outcomes were silently omitted. It is hardly far-fetched to propose that this drive to publish is contributing to the growth in the number of papers retracted from the literature for dubious conduct[9] along with the increasing number of cases of research misconduct.

Reproducibility and transparency in biomedical sciences

The biomedical research sciences are currently facing a challenge highlighted in several recent publications: concerns about the rigor and reproducibility of studies published in the scientific literature.Research progress is strongly dependent on published work. Basic science researchers build on their own prior work and the published findings of other researchers. This work becomes the foundation for preclinical and clinical research aimed at developing innovative new diagnostic tools and disease therapies. At each of the stages of research, scientific rigor and reproducibility are critical, and the financial and ethical stakes rise as drug development research moves through these stages.

Most computational hydrology is not reproducible, so is it really science?

Reproducibility is a foundational principle in scientific research. Yet in computational hydrology, the code and data that actually produces published results is not regularly made available, inhibiting the ability of the community to reproduce and verify previous findings. In order to overcome this problem we recommend that re-useable code and formal workflows, which unambiguously reproduce published scientific results, are made available for the community alongside data, so that we can verify previous findings, and build directly from previous work. In cases where reproducing large-scale hydrologic studies is computationally very expensive and time-consuming, new processes are required to ensure scientific rigour. Such changes will strongly improve the transparency of hydrological research, and thus provide a more credible foundation for scientific advancement and policy support.

Scientific Misconduct: The Elephant in the Lab. A Response to Parker et al.

In a recent Opinion article, Parker et al. [1] highlight a range of important issues and provide tangible solutions to improve transparency in ecology and evolution (E&E). We agree wholeheartedly with their points and encourage the E&E community to heed their advice. However, a key issue remains conspicuously unaddressed: Parker et al. assume that ‘deliberate dishonesty’ is rare in E&E, yet evidence suggests that occurrences of scientific misconduct (i.e., data fabrication, falsification, and/or plagiarism) are disturbingly common in the life sciences [2].