Related papers: Impacting the bioscience progress by backporting s…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
Provided that there is no theoretical frame for complex engineered systems (CES) as yet, this paper claims that bio-inspired engineering can help provide such a frame. Within CES bio-inspired systems play a key role. The disclosure from…
"Evolution behaves like a tinkerer" (Francois Jacob, Science, 1977). Software systems provide a unique opportunity to understand biological processes using concepts from network theory. The Debian GNU/Linux operating system allows us to…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
Patch backporting, the process of migrating mainline security patches to older branches, is an essential task in maintaining popular open-source projects (e.g., Linux kernel). However, manual backporting can be labor-intensive, while…
Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example,…
In the last few decades or so, we witness a paradigm shift in our nature studies - from a data-processing based computational approach to an information-processing based cognitive approach. The process is restricted and often misguided by…
Containers are an emerging technology that hold promise for improving productivity and code portability in scientific computing. We examine Linux container technology for the distribution of a non-trivial scientific computing software stack…
We introduce a unified Python package for the prediction of protein biophysical properties, streamlining previous tools developed by the Bio2Byte research group. This suite facilitates comprehensive assessments of protein characteristics,…
This study examines the impact of GitHub Copilot on a large sample of Copilot users (n=934,533). The analysis shows that users on average accept nearly 30% of the suggested code, leading to increased productivity. Furthermore, our research…
Source code repositories allow developers to manage multiple versions (or branches) of a software system. Pull-requests are used to modify a branch, and backporting is a regular activity used to port changes from a current development…
Modern tools for biological research, especially microscopy, have rapidly advanced in recent years, which has led to the generation of increasingly large amounts of data on a regular basis. The result is that scientists desperately need…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
Bioinformatics is a new discipline that addresses the need to manage and interpret the data that in the past decade was massively generated by genomic research. This discipline represents the convergence of genomics, biotechnology and…
Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered…
The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored…
Software systems situated in network environment may experience performance degradation, availability decrease and even crash during long time running, which is called software aging. This phenomenon has been studied for more than 15 years,…
Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require…
Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…