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In recent years, the research community has raised serious questions about the reproducibility of scientific work. In particular, since many studies include some kind of computing work, reproducibility is also a technological challenge, not…
With the goal of identifying common practices in data science projects, this paper proposes a framework for logging and understanding incremental code executions in Jupyter notebooks. This framework aims to allow reasoning about how…
Unlike static documents, version-controlled documents are edited by one or more authors over a certain period of time. Examples include large scale computer code, papers authored by a team of scientists, and online discussion boards. Such…
Scholarly writing presents a complex space that generally follows a methodical procedure to plan and produce both rationally sound and creative compositions. Recent works involving large language models (LLM) demonstrate considerable…
Reproducibility is widely acknowledged as a fundamental principle in scientific research. Currently, the scientific community grapples with numerous challenges associated with reproducibility, often referred to as the ''reproducibility…
An issue tracker is a software tool used by organisations to interact with users and manage various aspects of the software development lifecycle. With the rise of agile methodologies, issue trackers have become popular in open and…
Peer review is a key component of the publishing process in most fields of science. The increasing submission rates put a strain on reviewing quality and efficiency, motivating the development of applications to support the reviewing and…
The ability to repeat the experiments from a research study and obtain similar results is a corner stone in experiment-based scientific discovery. This essential feature has been often ignored by the distributed computing and networking…
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…
Reproducibility in research remains hindered by complex systems involving data, models, tools, and algorithms. Studies highlight a reproducibility crisis due to a lack of standardized reporting, code and data sharing, and rigorous…
As computer systems grow ever larger and more complex, a crucial task in software development is for one person (the system expert) to communicate to another (the system novice) how a certain program works. This paper reports on the…
This paper proposes a procedure to execute external source codes from a LaTeX document and include the calculation outputs in the resulting Portable Document Format (pdf) file automatically. It integrates programming tools into the LaTeX…
The rapid growth of preprint servers has accelerated scientific dissemination but has also shifted the technical burden of manuscript preparation to authors. This challenge is particularly acute in computational research, where manuscripts…
Huge amount of information is present in the World Wide Web and a large amount is being added to it frequently. A query-specific summary of multiple documents is very helpful to the user in this context. Currently, few systems have been…
Science progresses by building upon the prior body of knowledge documented in scientific publications. The acceleration of research makes it hard to stay up-to-date with the recent developments and to summarize the ever-growing body of…
The vast majority of scientific contributions in the field of computational systems biology are based on mathematical models. These models can be broadly classified as either dynamic (kinetic) models or steady-state (constraint-based)…
Software documentation captures detailed knowledge about a software product, e.g., code, technologies, and design. It plays an important role in the coordination of development teams and in conveying ideas to various stakeholders. However,…
Motivation: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between…
"Computational experiments" use code and interactive visualizations to convey mathematical and physical concepts in an intuitive way, and are increasingly used to support ex cathedra lecturing in scientific and engineering disciplines.…
A software release note is one of the essential documents in the software development life cycle. The software release contains a set of information, e.g., bug fixes and security fixes. Release notes are used in different phases, e.g.,…