This presentation to LERU workshop: Nurturing a Culture of Responsible Research in the Era of Open Science considered the issue of the credibility of science being in question in a 'post-truth' world and how reproducibility is adding to the problem. Open Science offers a solution, but it is not easy to implement, particularly by research institutions. The main issues relate to language used in the open space, that solutions look different to different disciplines, that researchers are often feeling "under siege" and that we need to reward good open practice.
A fundamental challenge for open science is how best to create and share documents containing computational results. Traditional methods involve maintaining the code, generated tables and figures, and text as separate files and manually assembling them into a finished document. As projects grow in complexity, this approach can lead to procedures which are error prone and hard to replicate. Fortunately, new tools are emerging to address this problem and librarians who provide data services are ideally positioned to provide training. In the workshop we’ll use RStudio to demonstrate how to create a "compilable" document containing all the text elements (including bibliography), as well as the code required to create embedded graphs and tables. We’ll demonstrate how the process facilitates making revisions when, for example, a reviewer has suggested a revision or when there has been a change in the underlying data. We’ll also demonstrate the convenience of integrating version control into the workflow using RStudio’s built-in support for git.
Presentation given for Love Data Week 2018.
Open access to research data increases knowledge, advances science, and benefits society. Many researchers are now required to share data. Two research centers at Yale have launched projects that support this mission. Both centers have developed technology, policies, and workflows to facilitate open access to data in their respective fields. The Yale University Open Data Access (YODA) Project at the Center for Outcomes Research and Evaluation advocates for the responsible sharing of clinical research data. The Project, which began in 2014, is committed to open science and data transparency, and supports research attempting to produce concrete benefits to patients, the medical community, and society as a whole. Early experience sharing data, made available by Johnson & Johnson (J&J) through the YODA Project, has demonstrated a demand for shared clinical research data as a resource for investigators. To date, the YODA Project has facilitated the sharing of data for over 65 research projects. The Institution for Social and Policy Studies (ISPS) Data Archive is a digital repository that shares and preserves the research produced by scholars affiliated with ISPS. Since its launch in 2011, the Archive holds data and code underlying almost 90 studies. The Archive is committed to the ideals of scientific reproducibility and transparency: It provides free and public access to research materials and accepts content for distribution under a Creative Commons license. The Archive has pioneered a workflow, “curating for reproducibility,” that ensures long term usability and data quality.
Workshop in methods at IU.
A presentation by Mohammad Akhlaghi from the Centre de Recherche Astrophysique de Lyon (CRAL) on reproducibility through using Make.