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The rise of advanced chatbots, such as ChatGPT, has sparked curiosity in the scientific community. ChatGPT is a general-purpose chatbot powered by large language models (LLMs) GPT-3.5 and GPT-4, with the potential to impact numerous fields,…
Computers are a very important part of our lives and the major reason why they have been such a success is because of the excellent graphical operating systems that run on these powerful machines. As the computer hardware is becoming more…
Maintaining software is an ongoing process that stretches beyond the initial release. Stable software versions continuously evolve to fix bugs, add improvements, address security issues, and ensure compatibility. This ongoing support…
The popularity and wide spread of IoT technology has brought about a rich hardware infrastructure over which it is possible to run powerful applications that were not previously imagined. Among this infrastructure, there are the medical…
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking, and dependency management. To manage these processes, a diverse set…
The increasing popularity of AI, particularly Large Language Models (LLMs), has significantly impacted various domains, including Software Engineering. This study explores the integration of AI tools in software engineering practices within…
Scientific applications in HPC environment are more com-plex and more data-intensive nowadays. Scientists usually rely on workflow system to manage the complexity: simply define multiple processing steps into a single script and let the…
Although there was an early experiment in the 1960s with the central distribution of paper preprints in the biomedical sciences, these sciences have not been early adopters of electronic preprint servers. Some barriers to the development of…
The Accelerator Control System at Fermilab has evolved to enable this relatively large control system to be encapsulated into a "box" such as a laptop. The goal was to provide a platform isolated from the "online" control system. This…
In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research…
An Operating System (OS) combines multiple interdependent software packages, which usually have their own independently developed architectures. When a multitude of independent packages are placed together in an OS, an implicit…
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…
Measuring and analyzing the performance of software has reached a high complexity, caused by more advanced processor designs and the intricate interaction between user programs, the operating system, and the processor's microarchitecture.…
Our planet is experiencing an accelerated process of change associated to a variety of anthropogenic phenomena. The future of this transformation is uncertain, but there is general agreement about its negative unfolding that might threaten…
Open-source software is a complex system; its development depends on the self-coordinated action of a large number of agents. This study follows the size of the building blocks, called "packages", of the Ubuntu Linux operating system over…
The rapid advancements in quantum computing necessitate a scientific and rigorous approach to the construction of a corresponding software ecosystem, a topic underexplored and primed for systematic investigation. This chapter takes an…
Laboratory research is a complex, collaborative process that involves several stages, including hypothesis formulation, experimental design, data generation and analysis, and manuscript writing. Although reproducibility and data sharing are…
Motivation: Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base construction and protein structure determination all benefit from human input. In…
We present Rust-Bio, the first general purpose bioinformatics library for the innovative Rust programming language. Rust-Bio leverages the unique combination of speed, memory safety and high-level syntax offered by Rust to provide a fast…
Many modern software projects evolve rapidly to incorporate new features and security patches. It is important for users to update their dependencies to safer versions, but many still use older, vulnerable package versions because upgrading…