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With the increasing amount of data and use of computation in science, software has become an important component in many different domains. Computing is now being used more often and in more aspects of scientific work including data…
In a new effort to make our research transparent and reproducible by others, we developed a workflow to run and share computational studies on the public cloud Microsoft Azure. It uses Docker containers to create an image of the application…
Notebooks provide an author-friendly environment for iterative development, modular execution, and easy sharing. Distributed workflows are increasingly being authored and executed in notebooks, yet sharing and reproducing them remains…
How many times have you tried to re-implement a past CAV tool paper, and failed? Reliably reproducing published scientific discoveries has been acknowledged as a barrier to scientific progress for some time but there remains only a small…
Jupyter notebooks represent a unique format for programming - a combination of code and Markdown with rich formatting, separated into individual cells. We propose to perceive a Jupyter Notebook cell as a simplified and raw version of a…
As access to the internet has become increasingly ubiquitous, along with the reliability and speed of internet providers, so too has the implementation of internet-based learning tools. These tools provide students opportunities to do…
The general purpose of a scientific publication is the exchange and spread of knowledge. A publication usually reports a scientific result and tries to convince the reader that it is valid. With an ever-growing number of papers relying on…
Complex scientific codes and the datasets they generate are in need of a sophisticated categorization environment that allows the community to store, search, and enhance metadata in an open, dynamic system. Currently, data is often…
The ability to cite software and give credit to its authors and contributors is increasingly important. While the number of online open-source software repositories has grown rapidly over the past few years, few are being properly cited…
The field of scientific publishing that is served by LaTeX is increasingly dependent on the availability of metadata about publications. We discuss how to use LaTeX classes and BibTeX styles to curate metadata throughout the life cycle of a…
Computational tools for data analysis are being released daily on repositories such as the Comprehensive R Archive Network. How we integrate these tools to solve a problem in research is increasingly complex and requiring frequent updates.…
Life sciences research depends heavily on open-source academic software, yet many tools remain underused due to practical barriers. These include installation requirements that hinder adoption and limited developer resources for software…
Undergraduate programs in science and engineering include at least one course in basic programming, but seldom presented in a contextualized format, where computing is a tool for thinking and learning in the discipline. We have created a…
Scientific processes rely on software as an important tool for data acquisition, analysis, and discovery. Over the years sustainable software development practices have made progress in being considered as an integral component of research.…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
Diverse presentation formats play a pivotal role in effectively conveying code and analytical processes during data analysis. One increasingly popular format is tutorial videos, particularly those based on Jupyter notebooks, which offer an…
The reproduction and replication of reported scientific results is a hot topic within the academic community. The retraction of numerous studies from a wide range of disciplines, from climate science to bioscience, has drawn the focus of…
Citing data and software is a means to give scholarly credit and to facilitate access to research objects. Citation principles encourage authors to provide full descriptions of objects, with stable links, in their papers. As Jupyter…
Developers in data science and other domains frequently use computational notebooks to create exploratory analyses and prototype models. However, they often struggle to incorporate existing software engineering tooling into these…
Dockerfiles are one of the most prevalent kinds of DevOps artifacts used in industry. Despite their prevalence, there is a lack of sophisticated semantics-aware static analysis of Dockerfiles. In this paper, we introduce a dataset of…