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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…
Traditionally, statistical computing courses have taught the syntax of a particular programming language or specific statistical computation methods. Since the publication of Nolan and Temple Lang (2010), we have seen a greater emphasis on…
In the past decade, enormous progress has been made in advancing the state-of-the-art in bioimage analysis - a young computational field that works in close collaboration with the life sciences on the quantitative analysis of scientific…
Statistical analysis is the tool of choice to turn data into information, and then information into empirical knowledge. To be valid, the process that goes from data to knowledge should be supported by detailed, rigorous guidelines, which…
The experimental evaluation of the methods and concepts covered in software engineering has been increasingly valued. This value indicates the constant search for new forms of assessment and validation of the results obtained in Software…
The reproduction and replication of novel results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the issues closely revolve around the…
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…
Software Engineering and the implementation of software has become a challenging task as many tools, frameworks and languages must be orchestrated into one functioning piece. This complexity increases the need for testing and analysis…
We have been thinking about other aspects of software engineering for many years; the missing link in engineering software is the soft skills set, essential in the software development process. Although soft skills are among the most…
Software is becoming a critical component of most products and organizational functions. The ability to continuously improve software determines how well the organization can respond to market opportunities. Continuous software engineering…
Software is now a vital scientific instrument, providing the tools for data collection and analysis across disciplines from bioinformatics and computational physics, to the humanities. The software used in research is often home-grown and…
The growing emphasis on studying equity, diversity, and inclusion within software engineering has amplified the need to explore hidden populations within this field. Exploring hidden populations becomes important to obtain invaluable…
Probabilistic programming is a growing area that strives to make statistical analysis more accessible, by separating probabilistic modelling from probabilistic inference. In practice this decoupling is difficult. No single inference…
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…
Software is vital for the advancement of biology and medicine. Analysis of usage and impact metrics can help developers determine user and community engagement, justify additional funding, encourage additional use, identify unanticipated…
Software security has been an important research topic over the years. The community has proposed processes and tools for secure software development and security analysis. However, a significant number of vulnerabilities remains in…
Software product lines have recently been presented as one of the best promising improvements for the efficient software development. Different research works contribute supportive parameters and negotiations regarding the problems of…
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…
Writing complex computer programs to study scientific problems requires careful planning and an in-depth knowledge of programming languages and tools. In this chapter the importance of using the right tool for the right problem is…
This paper explores the intricate challenge of understanding and measuring software engineer behavior. More specifically, we revolve around a central question: How can we enhance our understanding of software engineer behavior? Grounded in…