Related papers: Re-run, Repeat, Reproduce, Reuse, Replicate: Trans…
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…
Academic software development practices often differ from those of commercial development settings, yet only limited research has been conducted on assessing software development practises in academia. Here we present a case study of…
Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being…
Reproducibility should be a cornerstone of scientific research and is a growing concern among the scientific community and the public. Understanding how to design services and tools that support documentation, preservation and sharing is…
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…
Refactoring is the de-facto practice to optimize software health. While several studies propose refactoring strategies to optimize software design through applying design patterns and removing design defects, little is known about how…
Reading computer program code and documentation written by others is, we are told, one of the best ways to learn the art of writing intelligible and maintainable code and documentation. The software resurrection exercise, introduced in this…
Program synthesis--the automated generation of executable code from high-level specifications--has been a central goal of computer science for over fifty years. This thesis provides a comparative literature review of the main paradigms that…
Background: Research software is crucial for enabling research discoveries and supporting data analysis, simulation, and interpretation across domains. However, evolving requirements, complex inputs, and legacy dependencies hinder the…
Research methods are essential parts in conducting any research project. Although they have been theorized and summarized based on best practices, every field of science requires an adaptation of the overall approaches to perform research…
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…
This article highlights how small modifications to either the source code of a benchmark program or the compilation options may impact its behavior on a specific machine. It argues that for evaluating machines, benchmark providers and users…
Although computer science papers are often accompanied by software artifacts, connecting research papers to their software artifacts and vice versa is not always trivial. First of all, there is a lack of well-accepted standards for how such…
Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, for executing the resulting automated workflows, and for recording the provenance of data products resulting…
In this note, I develop my personal view on the scope and relevance of symbolic computation in software science. For this, I discuss the interaction and differences between symbolic computation, software science, automatic programming,…
So far, the relationship between open science and software engineering expertise has largely focused on the open release of software engineering research insights and reproducible artifacts, in the form of open-access papers, open data, and…
Code summarization is the task of generating readable summaries that are semantically meaningful and can accurately describe the presumed task of a software. Program comprehension has become one of the most tedious tasks for knowledge…
In recent years, a series of high-profile retractions and fraud cases have arisen in physics, sparking a conversation about research integrity and replicability. Here, we discuss how the practice of science is shaped by the social and…
Open data and open-source software may be part of the solution to science's "reproducibility crisis", but they are insufficient to guarantee reproducibility. Requiring minimal end-user expertise, encapsulator creates a "time capsule" with…
Scientific software registries and repositories serve various roles in their respective disciplines. These resources improve software discoverability and research transparency, provide information for software citations, and foster…