Related papers: Scientific Software Engineering in a Nutshell

Scientific computation is a discipline that combines numerical analysis, physical understanding, algorithm development, and structured programming. Several yottacycles per year on the world's largest computers are spent simulating problems…

Science depends heavily on reliable and easy-to-use software packages, such as mathematical libraries or data analysis tools. Developing such packages requires a lot of effort, which is too often avoided due to the lack of funding or…

Context: Scientific software plays an important role in critical decision making, for example making weather predictions based on climate models, and computation of evidence for research publications. Recently, scientists have had to…

As computer systems become more and more complex, software and tools lag more and more behind. This is especially true for scientific software that often demands high performance, and thus needs to take advantage of parallelisms, memory…

Here practical aspects of conducting research via computer simulations are discussed. The following issues are addressed: software engineering, object-oriented software development, programming style, macros, make files, scripts, libraries,…

Computational methods and associated software implementations are central to every field of scientific investigation. Modern biological research, particularly within systems biology, has relied heavily on the development of software tools…

Scientific software-defined as computer programs, scripts, or code used in scientific research, data analysis, modeling, or simulation-has become central to modern research. However, there is limited research on the readability and…

Scientists spend an increasing amount of time building and using software. However, most scientists are never taught how to do this efficiently. As a result, many are unaware of tools and practices that would allow them to write more…

Background: Research software plays an important role in solving real-life problems, empowering scientific innovations, and handling emergency situations. Therefore, the correctness and trustworthiness of research software are of absolute…

Large language models (LLMs) have been touted to enable increased productivity in many areas of today's work life. Scientific research as an area of work is no exception: the potential of LLM-based tools to assist in the daily work of…

A large multitude of scientific computing tools is available today. This article gives an overview of available tools and explains the main application fields. In addition basic principles of number representations in computing and the…

Programming is ubiquitous in applied biostatistics; adopting software engineering skills will help biostatisticians do a better job. To explain this, we start by highlighting key challenges for software development and application in…

Scientific software often presents very particular requirements regarding usability, which is often completely overlooked in this setting. As computational science has emerged as its own discipline, distinct from theoretical and…

This article attempts to describe specific mental techniques that are related to resolving very complex tasks in software engineering. This subject may be familiar to some software specialists to different extents; however, there is…

In the last couple of years we have witnessed an enormous increase of machine learning (ML) applications. More and more program functions are no longer written in code, but learnt from a huge amount of data samples using an ML algorithm.…

A large number of computational scientific research projects make use of open source software packages. However, the development process of such tools frequently differs from conventional software development; partly because of the nature…

The vast majority of the long tail of scientific software, the myriads of tools that implement the many analysis and visualization methods for different scientific fields, is highly specialized, purpose-built for a research project, and has…

Scientific software is one of the key elements for reproducible research. However, classic publications and related scientific software are typically not (sufficiently) linked, and it lacks tools to jointly explore these artefacts. In this…

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 profile of research software engineering has been greatly enhanced by developments at institutions around the world to form groups and communities that can support effective, sustainable development of research software. We observe,…