Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.
Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.
Delivering cloud-like computing facilities at the network edge provides computing services with ultra-low-latency access, yielding highly responsive computing services to application requests. The concept of fog computing has emerged as a computing paradigm that adds layers of computing nodes between the edge and the cloud, also known as micro data centers, cloudlets, or fog nodes. Based on this premise, this paper proposes a component-based service scheduler in a cloud-fog computing infrastructure comprising several layers of fog nodes between the edge and the cloud. The proposed scheduler aims to satisfy the application's latency requirements by deciding which services components should be moved upwards in the fog-cloud hierarchy to alleviate computing workloads at the network edge. One communication-aware policy is introduced for resource allocation to enforce resource access prioritization among applications. We evaluate the proposal using the well-known iFogSim simulator. Results suggest that the proposed component-based scheduling algorithm can reduce average delays for application services with stricter latency requirements while still reducing the total network usage when applications exchange data between the components. Results have shown that our policy was able to, on average, reduce the overload impact on the network usage by approximately 11% compared to the best allocation policy in the literature while maintaining acceptable delays for latency-sensitive applications.
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