Related papers: GitHub is an effective platform for collaborative …
GitHub has become the central online platform for much of open source, hosting most open source code repositories. With this popularity, the public digital traces of GitHub are now a valuable means to study teamwork and collaboration. In…
DevOps is a combination of methodologies and tools that improves the software development, build, deployment, and monitoring processes by shortening its lifecycle and improving software quality. Part of this process is CI/CD, which embodies…
Continuous Integration (CI) has evolved from a tooling strategy to a fundamental mindset in modern CI engineering. It enables teams to develop, test, and deliver software rapidly and collaboratively. Among CI services, GitHub Actions (GHA)…
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
In the field of computational science and engineering, workflows often entail the application of various software, for instance, for simulation or pre- and postprocessing. Typically, these components have to be combined in arbitrarily…
Scientific advancement relies on the ability to share and reproduce results. When data analysis or calculations are carried out using software written by scientists there are special challenges around code versions, quality and code…
Science reproducibility is a cornerstone feature in scientific workflows. In most cases, this has been implemented as a way to exactly reproduce the computational steps taken to reach the final results. While these steps are often…
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…
The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS,…
Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require…
GitHub has become a popular social application platform, where a large number of users post their open source projects. In particular, an increasing number of researchers release repositories of source code related to their research papers…
While automated experiments and high-throughput methods are becoming more mainstream in the age of data, empowering individual researchers to capture, collate, and contextualize their data faster and more reproducibly still remains a…
Many fields of science rely on relational database management systems to analyze, publish and share data. Since RDBMS are originally designed for, and their development directions are primarily driven by, business use cases they often lack…
Reproducibility of computationally-derived scientific discoveries should be a certainty. As the product of several person-years' worth of effort, results -- whether disseminated through academic journals, conferences or exploited through…
Conducting experiments and documenting results is daily business of scientists. Good and traceable documentation enables other scientists to confirm procedures and results for increased credibility. Documentation and scientific conduct are…
GitHub, a central hub for collaborative software development, has revolutionized the open-source software (OSS) ecosystem through its GitHub Marketplace, a platform launched in 2017 to host automation tools aimed at enhancing the efficiency…
Science has a data management problem, as well as a project management problem. While industrial-grade data science teams have embraced the agile mindset, and adopted or created all kind of tools to create reproducible workflows,…
Continuous integration is a software engineering practice of frequently merging all developer working copies with a shared main branch, e.g., several times a day. With the advent of GitHub, a platform well known for its "social coding"…
Reusable data/code and reproducible analyses are foundational to quality research. This aspect, however, is often overlooked when designing interactive stream analysis workflows for time-series data (e.g., eye-tracking data). A mechanism to…
In recent years, the research community, but also the general public, has raised serious questions about the reproducibility and replicability of scientific work. Since many studies include some kind of computational work, these issues are…