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Since the turn of the millennium, computational modelling of biological systems has evolved remarkably and sees matured use spanning basic and clinical research. While the topic of the peri-millennial debate about the virtues and…
Software libraries are the elementary building blocks of open source software ecosystems, extending the capabilities of programming languages beyond their standard libraries. Although ecosystem health is often quantified using data on…
Within the field of biocybersecurity, it is important to understand what vulnerabilities may be uncovered in the processing of biologics as well as how they can be safeguarded as they intersect with cyber and cyberphysical systems, as noted…
We introduce Diffuse, a system that dynamically performs task and kernel fusion in distributed, task-based runtime systems. The key component of Diffuse is an intermediate representation of distributed computation that enables the necessary…
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…
The Hybrid Technology Hub and many other research centers work in cross-functional teams whose workflow is not necessarily linear and where in many cases technology advances are done through parallel work. The lack of proper tools and…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…
This paper introduces BioAgent Bench, a benchmark dataset and an evaluation suite designed for measuring the performance and robustness of AI agents in common bioinformatics tasks. The benchmark contains curated end-to-end tasks (e.g.,…
It is natural for humans to collaborate while dealing with complex problems. In this article I consider this process of collaboration in the context of information seeking. The study and discussion presented here are driven by two…
SUMMARY: Recently, novel machine-learning algorithms have shown potential for predicting undiscovered links in biomedical knowledge networks. However, dedicated benchmarks for measuring algorithmic progress have not yet emerged. With…
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…
There has been growing interest within the computational science and engineering (CSE) community in engaging with software engineering research -- the systematic study of software systems and their development, operation, and maintenance --…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
Critical goals of scientific computing are to increase scientific rigor, reproducibility, and transparency while keeping up with ever-increasing computational demands. This work presents an integrated framework well-suited for data…
Delivering effective data analytics is of crucial importance to the interpretation of the multitude of biological datasets currently generated by an ever increasing number of high throughput techniques. Logic programming has much to offer…
In this paper, we propose a novel system that integrates state-of-the-art, domain-specific large language models with advanced information retrieval techniques to deliver comprehensive and context-aware responses. Our approach facilitates…
Science advances not only through the accumulation of facts but also through the evolution of tools. Crucially, tools are rarely used in isolation. They form tool portfolios, combinations shaped by a discipline's workflows and analytical…
With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational…
While several paths have emerged in microelectronics and computing as follow-ons to Turing architectures, and have been implemented using essentially silicon circuits, very little beyond Moore research has considered: (1) first biological…
The evolution of the global scientific cyberinfrastructure (CI) has, over the last 10+ years, led to a large diversity of CI instances. While specialized, competing and alternative CI building blocks are inherent to a healthy ecosystem, it…