Related papers: Impacting the bioscience progress by backporting s…
The communities who develop and support open source scientific software packages are crucial to the utility and success of such packages. Moreover, these communities form an important part of the human infrastructure that enables scientific…
Despite the recent advancements in human-machine interfacing, contemporary assistive bionic limbs face critical challenges, including limited computational capabilities, high latency, and unintuitive control mechanisms, leading to…
[Context] AI assistants, like GitHub Copilot and Cursor, are transforming software engineering. While several studies highlight productivity improvements, their impact on maintainability requires further investigation. [Objective] This…
Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since,…
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…
Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is…
Managing the software complexity of package-based systems can be regarded as one of the main challenges in software architectures. Upgrades are required on a short time basis and systems are expected to be reliable and consistent after…
It is now five years since the launch of the International Journal of Bio-Inspired Computation (IJBIC). At the same time, significant new progress has been made in the area of bio-inspired computation. This review paper summarizes the…
In recent years, technology has advanced considerably with the introduction of many systems including advanced robotics, big data analytics, cloud computing, machine learning and many more. The opportunities to exploit the yet to come…
With the advances in e-Sciences and the growing complexity of scientific analyses, more and more scientists and researchers are relying on workflow systems for process coordination, derivation automation, provenance tracking, and…
Progress in science is deeply bound to the effective use of high-performance computing infrastructures and to the efficient extraction of knowledge from vast amounts of data. Such data comes from different sources that follow a cycle…
GitHub Copilot, an extension for the Visual Studio Code development environment powered by the large-scale language model Codex, makes automatic program synthesis available for software developers. This model has been extensively studied in…
Resilient cyber-physical systems comprise computing systems able to continuously interact with the physical environment in which they operate, despite runtime errors. The term resilience refers to the ability to cope with unexpected inputs…
How should software engineering be adapted for Computational Science (CS)? If we understood that, then we could better support software sustainability, verifiability, reproducibility, comprehension, and usability for CS community. For…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
Biophysics is a subject that is spread over many disciplines and transcends the skills and knowledge of the individual student. This makes it challenging both to teach and to learn. Educational materials are described to aid in teaching…
Language workbenches are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other…
Bio image analysis has recently become one keystone of biological research but biologists tend to get lost in a plethora of available software and the way to adjust available tools to their own image analysis problem. We present BIII,…