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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…
With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational…
The year 2023 marked a significant surge in the exploration of applying large language model (LLM) chatbots, notably ChatGPT, across various disciplines. We surveyed the applications of ChatGPT in bioinformatics and biomedical informatics…
In this paper we discuss the impact of open source on both the security and transparency of a software system. We focus on the more technical aspects of this issue, combining and extending arguments developed over the years. We stress that…
In this research, we present a comprehensive, longitudinal empirical summary of the R package ecosystem, including not just CRAN, but also Bioconductor and GitHub. We analyze more than 25,000 packages, 150,000 releases, and 15 million files…
We review various changes made in recent years to the software development process of the LAMMPS simulation software package and the software itself. We discuss how those changes have impacted the effort and workflow required to develop and…
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…
A growing gap between progress in biological knowledge and improved health outcomes inspired the new discipline of translational medicine, in which the application of new knowledge is an explicit part of a research plan. Abramson and…
This work-in-progress research paper explores the effectiveness of tutorials in interdisciplinary learning environments, specifically focusing on bioinformatics. Tutorials are typically designed for a single audience, but our study aims to…
The web ecosystem is rapidly evolving with changing business and functional models. Cloud platforms are available in a SaaS, PaaS and IaaS model designed around commoditized Linux based servers. 10 billion users will be online and accessing…
Pre-trained large language models (LLMs) have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks and to be appropriately specialized to particular…
The importance of computing in astronomy continues to increase, and so is its impact on the environment. When analyzing data or performing simulations, most researchers raise concerns about the time to reach a solution rather than its…
Although computer science papers are often accompanied by software artifacts, connecting research papers to their software artifacts and vice versa is not always trivial. First of all, there is a lack of well-accepted standards for how such…
Two years on from the initial release of AlphaFold2 we have seen its widespread adoption as a structure prediction tool. Here we discuss some of the latest work based on AlphaFold2, with a particular focus on its use within the structural…
There is a gap in scientific information systems development concerning modern software engineering and scientific computing. Historically, software engineering methodologies have been perceived as an unwanted accidental complexity to…
Nanoinformatics is a novel, rapidly growing area of research that involves the application of computational techniques to several aspects of research in the field of nanotechnology, especially concerned its application to biotechnology.…
Understanding large molecular networks consisting of entities such as genes, proteins or RNAs that interact in complex ways to drive the cellular machinery has been an active focus of systems biology. Computational approaches have played a…
Assuring traceability from requirements to implementation is a key element when developing safety critical software systems. Traditionally, this traceability is ensured by a waterfall-like process, where phases follow each other, and…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…
New model of software safety is offered. Distribution of mistakes in program on stages of life cycle is researched. Study of ways of increase of reliability of software at help simulation program is leaded.