Scientific progress relies on the replication and reuse of research. Recent studies suggest, however, that sharing code and data does not suffice for computational reproducibility —defined as the ability of researchers to reproduce “par- ticular analysis outcomes from the same data set using the same code and software” (Fidler and Wilcox, 2018). To date, creating long-term computationally reproducible code has been technically challenging and time-consuming. This tutorial introduces Code Ocean, a cloud-based computational reproducibility platform that attempts to solve these problems. It does this by adapting software engineering tools, such as Docker, for easier use by scientists and scientific audiences. In this article, we first outline arguments for the importance of computational reproducibility, as well as some reasons why this is a nontrivial problem for researchers. We then provide a step-by-step guide to getting started with containers in research using Code Ocean. (Disclaimer: the authors all worked for Code Ocean at the time of this article’s writing.)
Background: Complete and transparent reporting of clinical trial protocols and reports ensures that these documents are useful to all stakeholders, that bias is minimized, and that the research is not wasted. However, current studies repeatedly conclude that pediatric trial protocols and reports are not appropriately reported. Guidelines like SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) and CONSORT (Consolidated Standards of Reporting Trials) may improve reporting, but do not offer guidance on issues unique to pediatric trials. This paper reports two systematic reviews conducted to build the evidence base for the development of pediatric reporting guideline extensions: 1) SPIRIT-Children (SPIRIT-C) for pediatric trial protocols, and 2) CONSORT-Children (CONSORT-C) for pediatric trial reports. Method: MEDLINE, the Cochrane Methodology Register, and reference lists of included studies were searched. Publications of any type were eligible if they included explicit recommendations or empirical evidence for the reporting of potential items in a pediatric protocol (SPIRIT-C systematic review) or trial report (CONSORT-C systematic review). Study characteristics, recommendations and evidence for pediatric extension items were extracted. Recurrent themes in the recommendations and evidence were identified and synthesized. All steps were conducted by two reviewers. Results: For the SPIRIT-C and CONSORT-C systematic reviews 366 and 429 publications were included, respectively. Recommendations were identified for 48 of 50 original reporting items and sub-items from SPIRIT, 15 of 20 potential SPIRIT-C reporting items, all 37 original CONSORT items and sub-items, and 16 of 22 potential CONSORT-C reporting items. The following overarching themes of evidence to support or refute the utility of reporting items were identified:
NOTE: Accepted in principle at Meta-Psychology, submission number MP2018.892, link: https://osf.io/ps5ru/. Anyone can participate in peer review by sending the editor an email, or through discussion on social media. The preferred way of open commenting, however, is to use the hypothes.is integration at PsyArXiv and directly comment on this preprint. Editor: Rickard Carlsson, rickard.carlsson@lnu.seWebsite: https://open.lnu.se/index.php/metapsychology ABSTRACT: Scientific progress relies on the replication and reuse of research. However, despite an emerging culture of sharing code and data in psychology, the research practices needed to achieve computational reproducibility -- the quality of a research project entailing the provision of sufficient code, data and documentation to allow an independent researcher to re-obtain the project's results -- are not widely adopted. Historically, the ability to share and reuse computationally reproducible research was technically challenging and time-consuming. One welcome development on this front is the advent of containers, a technology intended to facilitate code sharing for software development. Containers, however, remain technically demanding and imperfectly suited for research applications. This editorial argues that the use of containers adapted for research can help foster a culture of reproducibiliy in psychology research. We will illustrate this by introducing Code Ocean, an online computational reproducibility platform. (Disclaimer: the authors work for Code Ocean.)
Background: Evidence suggests that newborn and child health systematic reviews and meta-analyses exhibit poor quality in reporting. The "Preferred Reporting Items in Systematic Review and Meta-Analysis" (PRISMA) and PRISMAProtocols (PRISMA-P) checklists have been developed to improve the reporting of systematic review results and protocols, respectively. We aimed to evaluate the clarity and transparency in reporting of child-centric items in child health systematic reviews (SRs) and SR protocols and to identify areas where reporting could be strengthened. Methods: Two preliminary lists of potential child-centric reporting items were used to examine current reporting. The Cochrane, DARE, MEDLINE, and EMBASE libraries were searched from 2010 to 2014 for systematic reviews that included children. Each report and protocol that met the inclusion criteria had their quality of reporting assessed by their reporting of child-centric items. Quality of reporting was assessed per whether one third, one to two thirds, or more than two thirds of papers complied with potential child-centric potential modifications/extensions to PRISMA and were analyzed by the following: (i) paper type (i.e., report vs. protocol), (ii) publication type (i.e., Cochrane vs. non-Cochrane), and (iii) population type (i.e., child-only vs. mixed populations vs. family/maternal).
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