Related papers: WinBioinfTools: Bioinformatics Tools for Windows H…

Biologists often perform clustering analysis to derive meaningful patterns, relationships, and structures from data instances and attributes. Though clustering plays a pivotal role in biologists' data exploration, it takes non-trivial…

Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To…

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…

In this paper, we present WildlifeDatasets (https://github.com/WildlifeDatasets/wildlife-datasets) - an open-source toolkit intended primarily for ecologists and computer-vision / machine-learning researchers. The WildlifeDatasets is…

We introduce bia-binder (BioImage Archive Binder), an open-source, cloud-architectured, and web-based coding environment tailored to bioimage analysis that is freely accessible to all researchers. The service generates easy-to-use Jupyter…

Application of deep learning on histopathological whole slide images (WSIs) holds promise of improving diagnostic efficiency and reproducibility but is largely dependent on the ability to write computer code or purchase commercial…

Advances in genome sequencing technologies generate massive amounts of sequence data that are increasingly analyzed and shared through public repositories. On-demand infrastructure services on cloud computing platforms enable the processing…

Despite the importance of scientific software for research, it is often not formally recognized and rewarded. This is especially true for foundational libraries, which are hidden below packages visible to the users (and thus doubly hidden,…

In the last few years,Brain-Computer Interfaces (BCIs) have progressed as an emerging research area in the fields of human-computer interaction and interactive systems.This is primarily due to the introduction of low-cost…

The widespread usage of Microsoft Windows has unfortunately led to a surge in malware, posing a serious threat to the security and privacy of millions of users. In response, the research community has mobilized, with numerous efforts…

Benchmarking, which involves collecting reference datasets and demonstrating method performances, is a requirement for the development of new computational tools, but also becomes a domain of its own to achieve neutral comparisons of…

Massive exploitation of next-generation sequencing technologies requires dealing with both: huge amounts of data and complex bioinformatics pipelines. Computing architectures have evolved to deal with these problems, enabling approaches…

Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…

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,…

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…

Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…

Microbiome studies have recently transitioned from experimental designs with a few hundred samples to designs spanning tens of thousands of samples. Modern studies such as the Earth Microbiome Project (EMP) afford the statistics crucial for…

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by…

Non-sharable sensitive data collection and analysis in large-scale consortia for genomic research is complicated. Time consuming issues in installing software arise due to different operating systems, software dependencies and running the…

Clustering is a popular data mining technique that aims to partition an input space into multiple homogeneous regions. There exist several clustering algorithms in the literature. The performance of a clustering algorithm depends on its…