Related papers: Full Computational Reproducibility in Biological S…
Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data…
In computational science and in computer science, research software is a central asset for research. Computational science is the application of computer science and software engineering principles to solving scientific problems, whereas…
The reproducibility of scientific articles is central to the advancement of science. Despite this importance, evaluating reproducibility remains challenging due to the scarcity of ground truth data. Predictive models can address this…
Computational models are increasingly used in high-impact decision making in science, engineering, and medicine. The National Aeronautics and Space Administration (NASA) uses computational models to perform complex experiments that are…
Scientific data governance should prioritize maximizing the utility of data throughout the research lifecycle. Research software systems that enable analysis reproducibility inform data governance policies and assist administrators in…
Reproducibility should be a cornerstone of science as it enables validation and reuse. In recent years, the scientific community and the general public became increasingly aware of the reproducibility crisis, i.e. the wide-spread inability…
Despite much creative work on methods and tools, reproducibility -- the ability to repeat the computational steps used to obtain a research result -- remains elusive. One reason for these difficulties is that extant tools for capturing…
The grand challenge of protein engineering is the development of computational models that can characterize and generate protein sequences for any arbitrary function. However, progress today is limited by lack of 1) benchmarks with which to…
The reproducibility of scientific experiment is vital for the advancement of disciplines based on previous work. To achieve this goal, many researchers focus on complex methodology and self-invented tools which have difficulty in practical…
We describe a project-based introduction to reproducible and collaborative neuroimaging analysis. Traditional teaching on neuroimaging usually consists of a series of lectures that emphasize the big picture rather than the foundations on…
Many in the Scientific Computing Software community believe that upfront requirements are impossible, or at least infeasible. This paper shows requirements are feasible with the following: i) an appropriate perspective ("faking" the final…
The integration of machine learning techniques in materials discovery has become prominent in materials science research and has been accompanied by an increasing trend towards open-source data and tools to propel the field. Despite the…
The issue of reproducibility of computational models and the related FAIR principles (findable, accessible, interoperable, and reusable) are examined in a specific test case. I analyze a computational model of the segment polarity network…
Scientific knowledge increasingly depends on complex computational processes where both hardware and software layers can influence research outcomes. As computational complexity grows, classical-quantum integration provides a lens for…
Computer simulations that demonstrate the valueof novel approaches are crucial to developing more flexibleand robust power systems operations with high penetrations ofrenewable energy at multiple geographic and temporal scales.However,…
Reproducibility has been consistently identified as an important component of scientific research. Although there is a general consensus on the importance of reproducibility along with the other commonly used 'R' terminology (i.e.,…
Reproducible computational research (RCR) is the keystone of the scientific method for in silico analyses, packaging the transformation of raw data to published results. In addition to its role in research integrity, RCR has the capacity to…
Why are some research studies easy to reproduce while others are difficult? Casting doubt on the accuracy of scientific work is not fruitful, especially when an individual researcher cannot reproduce the claims made in the paper. There…
Scientific investigation procedures have been evolving to follow an ever-changing cultural landscape, the sophistication of the technology available and an ever-growing knowledge base. This continuous evolution brought investigation…
Whole Tale http://wholetale.org is a web-based, open-source platform for reproducible research supporting the creation, sharing, execution, and verification of "Tales" for the scientific research community. Tales are executable research…