The contemporary scientific community places a growing emphasis on the reproducibility of research. The projects R package is a free, open-source endeavor created in the interest of facilitating reproducible research workflows. It adds to existing software tools for reproducible research and introduces several practical features that are helpful for scientists and their collaborative research teams. For each individual project, it supplies an intuitive framework for storing raw and cleaned study data sets, and provides script templates for protocol creation, data cleaning, data analysis and manuscript development. Internal databases of project and author information are generated and displayed, and manuscript title pages containing author lists and their affiliations are automatically generated from the internal database. File management tools allow teams to organize multiple projects. When used on a shared file system, multiple researchers can harmoniously contribute to the same project in a less punctuated manner, reducing the frequency of misunderstandings and the need for status updates.
Contemporary science faces many challenges in publishing results that are reproducible. This is due to increased usage of data and digital technologies as well as heightened demands for scholarly communication. These challenges have led to widespread calls for more research transparency, accessibility, and reproducibility from the science community. This article presents current findings and solutions to these problems, including recent new software that makes writing submission-ready manuscripts for journals of Copernicus Publications a lot easier.
Most efforts to estimate the reproducibility of published findings have focused on specific areas of research, even though science is usually assessed and funded on a regional or national basis. Here we describe a project to assess the reproducibility of findings in biomedical science published by researchers based in Brazil. The Brazilian Reproducibility Initiative is a systematic, multi-center effort to repeatbetween 60 and 100 experiments: theproject will focus on a set of common laboratory methods, repeating each experiment in three different laboratories. The results, due in 2021, will allow us to estimate the level of reproducibility of biomedical sciencein Brazil, and to investigate what the published literature can tell us about the reproducibility ofresearch in a given area.
As databases of medical information are growing, the cost of analyzing data is falling, and computer scientists, engineers, and investment are flooding into the field, digital medicine is subject to increasingly hyperbolic claims. Every week brings news of advances: superior algorithms that can predict clinical events and disease trajectory, classify images better than humans, translate clinical texts, and generate sensational discoveries around new risk factors and treatment effects. Yet the excitement about digital medicine—along with the technologies like the ones that enable a million people to watch a major event—poses risks for its robustness. How many of those new findings, in other words, are likely to be reproducible?
Docker seems to be an attractive solution for cloud database benchmarking as it simplifies the setup process through pre-built images that are portable and simple to maintain. However, the usage of Docker for benchmarking is only valid if there is no effect on measurement results. Existing work has so far only focused on the performance overheads that Docker directly induces for specific applications. In this paper, we have studied indirect effects of dockerization on the results of database benchmarking. Among others, our results clearly show that containerization has a measurable and non-constant influence on measurement results and should, hence, only be used after careful analysis.
These 10 simple rules should not be limited to molecular dynamics but also include Monte Carlo simulations, quantum mechanics calculations, molecular docking, and any other computational methods involving computations on biological molecules.