Related papers: GlobDB: A comprehensive species-dereplicated micro…
In hierarchical structure formation, the content of a galaxy is determined both by its in-situ processes and by material added via accretions. Globular clusters in particular represent a window for the study of the different merger events…
Lifemapper (http://www.lifemapper.org) is a predictive electronic atlas of the Earth's biological biodiversity. Using a screensaver version of the GARP genetic algorithm for modeling species distributions, Lifemapper harnesses vast…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…
We make a case for "planetary computing" -- infrastructure to handle the ingestion, transformation, analysis and publication of global data products for furthering environmental science and enabling better informed policy-making. We draw on…
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists due to its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina…
Complex wounds usually face partial or total loss of skin thickness, healing by secondary intention. They can be acute or chronic, figuring infections, ischemia and tissue necrosis, and association with systemic diseases. Research…
In this paper we present a new family of Intensional RDBs (IRDBs) which extends the traditional RDBs with the Big Data and flexible and 'Open schema' features, able to preserve the user-defined relational database schemas and all…
We introduce TurboGP, a Genetic Programming (GP) library fully written in Python and specifically designed for machine learning tasks. TurboGP implements modern features not available in other GP implementations, such as island and cellular…
As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive…
Current extragalactic databases are reviewed, including object-oriented databases, astronomical catalogues and compilations, as well as image archives and object catalogues from large-scale surveys. One challenge of the future will be to…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Globular clusters are found usually in galaxies and they are an excellent tracer of dark matter. Long ago it was suggested that there may exist intracluster globular clusters (IGCs) bound to a galaxy cluster rather than to any single…
Microbiome data analysis is essential for understanding host health and disease, yet its inherent sparsity and noise pose major challenges for accurate imputation, hindering downstream tasks such as biomarker discovery. Existing imputation…
We describe a new interactive database (GRDB) of geometric objects in the general area of differential geometry. Database objects include, but are not restricted to, exact solutions of Einstein's field equations. GRDB is designed for…
Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area…
Research data are often released upon journal publication to enable result verification and reproducibility. For that reason, research dissemination infrastructures typically support diverse datasets coming from numerous disciplines, from…
A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation results. We manually drew a comprehensive map, ReconMap 2.0,…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
In biomedical research, validation of a new scientific discovery is tied to the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility still remain imprecise. Here, we argue…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…