Related papers: GlobDB: A comprehensive species-dereplicated micro…
Crowdsourcing is a multidisciplinary research area including disciplines like artificial intelligence, human-computer interaction, database, and social science. To facilitate cooperation across disciplines, reproducibility is a crucial…
Researchers in biomedical research, public health, and the life sciences often spend weeks or months discovering, accessing, curating, and integrating data from disparate sources, significantly delaying the onset of actual analysis and…
Today's HPC installations are highly-complex systems, and their complexity will only increase as we move to exascale and beyond. At each layer, from facilities to systems, from runtimes to applications, a wide range of tuning decisions must…
Summary: Data management in clinical metabolomics studies is often inadequate. To improve this situation we created LabPipe to provide a guided, customisable approach to study-specific sample collection. It is driven through a local client…
Pattern-based file access is a fundamental but often under-documented aspect of computational research. The Python glob module provides a simple yet powerful way to search, filter, and ingest files using wildcard patterns, enabling scalable…
Statistical analysis of distributions of occurrence frequencies of short words in 108 microbial complete genomes reveals the existence of a set of universal "root-sequence lengths" shared by all microbial genomes. These lengths and their…
We describe an online database for extra-solar planetary-mass candidates, updated regularly as new data are available. We first discuss criteria for the inclusion of objects in the catalog: "definition" of a planet and several aspects of…
We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples, and to prepare these cells for bulk whole genome sequencing without cultivation. We characterize this approach by…
The NIH Human BioMolecular Atlas Program (HuBMAP) Data Portal (https://portal.hubmapconsortium.org/) serves as a comprehensive repository for multi-modal spatial and single-cell data from healthy human tissues. This resource facilitates the…
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…
The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools…
Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational…
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…
Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable…
Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…
Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the…
Ascertaining the feasibility of independent falsification or repetition of published results is vital to the scientific process, and replication or reproduction experiments are routinely performed in many disciplines. Unfortunately, such…
We introduce 3DB: an extendable, unified framework for testing and debugging vision models using photorealistic simulation. We demonstrate, through a wide range of use cases, that 3DB allows users to discover vulnerabilities in computer…