Related papers: The Updated Genome Warehouse: Enhancing Data Value…
Over the past years, substantial numbers of microbial species' genomes have been deposited outside of conventional INSDC databases. The GlobDB aggregates 14 independent genomic catalogues to provide a comprehensive database of…
Background: The secure management of sensitive clinical data, particularly human genomics data, has become a critical requirement in modern biomedical research. Although the necessary software and algorithms are readily available, their use…
Recent studies demonstrate that effective healthcare can benefit from using the human genomic information. For instance, analysis of tumor genomes has revealed 140 genes whose mutations contribute to cancer. As a result, many institutions…
While the publication of datasets in scientific repositories has become broadly recognised, the repositories tend to have increasing semantic-related problems. For instance, they present various data reuse obstacles for machine-actionable…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
The availability of network datasets advances research in network science, machine learning and related fields by enabling empirical analyses and their reproducibility, algorithm development, model validation and benchmarking. Existing…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…
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…
The building sector plays a crucial role in the worldwide decarbonization effort, accounting for significant portions of energy consumption and environmental effects. However, the scarcity of open data sources is a continuous challenge for…
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…
Hash tables are ubiquitous. Properties such as an amortized constant time complexity for insertion and querying as well as a compact memory layout make them versatile associative data structures with manifold applications. The rapidly…
Motivation: The rapid growth in genome-wide association studies (GWAS) in plants and animals has brought about the need for a central resource that facilitates i) performing GWAS, ii) accessing data and results of other GWAS, and iii)…
The data revolution holds significant promise for the health sector. Vast amounts of data collected from individuals will be transformed into knowledge, AI models, predictive systems, and best practices. One area of health that stands to…
Many fields of science rely on relational database management systems to analyze, publish and share data. Since RDBMS are originally designed for, and their development directions are primarily driven by, business use cases they often lack…
Progress in Whole Genome Sequencing (WGS) will soon allow a large number of individuals to have their genome fully sequenced. This lays the foundations to improve modern healthcare, enabling a new era of personalized medicine where…
Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted…
The cost of DNA sequencing has resulted in a surge of genetic data being utilised to improve scientific research, clinical procedures, and healthcare delivery in recent years. Since the human genome can uniquely identify an individual, this…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
We introduce the Software Heritage filesystem (SwhFS), a user-space filesystem that integrates large-scale open source software archival with development workflows. SwhFS provides a POSIX filesystem view of Software Heritage, the largest…