Posts about reproducible paper (old posts, page 7)

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research†

With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

A Guide to Reproducibility in Preclinical Research

Many have raised concerns about the reproducibility of biomedical research. In this Perspective, the authors address this "reproducibility crisis" by distilling discussions around reproducibility into a simple guide to facilitate understanding of the topic.Reproducibility applies both within and across studies. The following questions address reproducibility within studies: "Within a study, if the investigator repeats the data management and analysis will she get an identical answer?" and "Within a study, if someone else starts with the same raw data, will she draw a similar conclusion?" Contrastingly, the following questions address reproducibility across studies: "If someone else tries to repeat an experiment as exactly as possible, will she draw a similar conclusion?" and "If someone else tries to perform a similar study, will she draw a similar conclusion?"Many elements of reproducibility from clinical trials can be applied to preclinical research (e.g., changing the culture of preclinical research to focus more on transparency and rigor). For investigators, steps toward improving reproducibility include specifying data analysis plans ahead of time to decrease selective reporting, more explicit data management and analysis protocols, and increasingly detailed experimental protocols, which allow others to repeat experiments. Additionally, senior investigators should take greater ownership of the details of their research (e.g., implementing active laboratory management practices, such as random audits of raw data [or at least reduced reliance on data summaries], more hands-on time overseeing experiments, and encouraging a healthy skepticism from all contributors). These actions will support a culture where rigor + transparency = reproducibility.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.

Preserving Workflow Reproducibility: The RePlay-DH Client as a Tool for Process Documentation

In this paper we present a software tool for elicitation and management of process metadata. It follows our previously published design idea of an assistant for researchers that aims at minimizing the additional effort required for producing a sustainable workflow documentation. With the ever-growing number of linguistic resources available, it also becomes increasingly important to provide proper documentation to make them comparable and to allow meaningful evaluations for specific use cases. The often prevailing practice of post hoc documentation of resource generation or research processes bears the risk of information loss. Not only does detailed documentation of a process aid in achieving reproducibility, it also increases usefulness of the documented work for others as a cornerstone of good scientific practice. Time pressure together with the lack of simple documentation methods leads to workflow documentation in practice being an arduous and often neglected task. Our tool ensures a clean documentation for common workflows in natural language processing and digital humanities. Additionally, it can easily be integrated into existing institutional infrastructures.

Writing Empirical Articles: Transparency, Reproducibility, Clarity, and Memorability

This article provides recommendations for writing empirical journal articles that enable transparency, reproducibility, clarity, and memorability. Recommendations for transparency include preregistering methods, hypotheses, and analyses; submitting registered reports; distinguishing confirmation from exploration; and showing your warts. Recommendations for reproducibility include documenting methods and results fully and cohesively, by taking advantage of open-science tools, and citing sources responsibly. Recommendations for clarity include writing short paragraphs, composed of short sentences; writing comprehensive abstracts; and seeking feedback from a naive audience. Recommendations for memorability include writing narratively; embracing the hourglass shape of empirical articles; beginning articles with a hook; and synthesizing, rather than Mad Libbing, previous literature.

A Primer on the ‘Reproducibility Crisis’ and Ways to Fix It

This article uses the framework of Ioannidis (2005) to organise a discussion of issues related to the ‘reproducibility crisis’. It then goes on to use that framework to evaluate various proposals to fix the problem. Of particular interest is the ‘post‐study probability’, the probability that a reported research finding represents a true relationship. This probability is inherently unknowable. However, a number of insightful results emerge if we are willing to make some conjectures about reasonable parameter values. Among other things, this analysis demonstrates the important role that replication can play in improving the signal value of empirical research.

A Statistical Model to Investigate the Reproducibility Rate Based on Replication Experiments

The reproducibility crisis, that is, the fact that many scientific results are difficult to replicate, pointing to their unreliability or falsehood, is a hot topic in the recent scientific literature, and statistical methodologies, testing procedures and p‐values, in particular, are at the centre of the debate. Assessment of the extent of the problem–the reproducibility rate or the false discovery rate–and the role of contributing factors are still an open problem. Replication experiments, that is, systematic replications of existing results, may offer relevant information on these issues. We propose a statistical model to deal with such information, in particular to estimate the reproducibility rate and the effect of some study characteristics on its reliability. We analyse data from a recent replication experiment in psychology finding a reproducibility rate broadly coherent with other assessments from the same experiment. Our results also confirm the expected role of some contributing factor (unexpectedness of the result and room for bias) while they suggest that the similarity between original study and the replica is not so relevant, thus mitigating some criticism directed to replication experiments.