Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project

We present biallelic SNVs called from 2,548 samples across 26 populationsfrom the 1000 Genomes Project, called directly on GRCh38. We believethis will be a useful reference resource for those using GRCh38,representing an improvement over the “lift-overs” of the 1000 GenomesProject data that have been available to date and providing a resourcenecessary for the full adoption of GRCh38 by the community. Here, wedescribe how the call set was created and provide benchmarking datadescribing how our call set compares to that produced by the final phase ofthe 1000 Genomes Project on GRCh37

Constant Angular Velocity Regulation for Visually Guided Terrain Following

Insects use visual cues to control their flight behaviours. By estimating the angular velocity of the visual stimuli and regulating it to a constant value, honeybees can perform a terrain following task which keeps the certain height above the undulated ground. For mimicking this behaviour in a bio-plausible computation structure, this paper presents a new angular velocity decoding model based on the honeybee's behavioural experiments. The model consists of three parts, the texture estimation layer for spatial information extraction, the motion detection layer for temporal information extraction and the decoding layer combining information from pervious layers to estimate the angular velocity. Compared to previous methods on this field, the proposed model produces responses largely independent of the spatial frequency and contrast in grating experiments. The angular velocity based control scheme is proposed to implement the model into a bee simulated by the game engine Unity. The perfect terrain following above patterned ground and successfully flying over irregular textured terrain show its potential for micro unmanned aerial vehicles' terrain following

Towards Computational Models and Applications of Insect Visual Systems for Motion Perception: A Review

Motion perception is a critical capability determining a variety of aspects of insects' life, including avoiding predators, foraging and so forth. A good number of motion detectors have been identified in the insects' visual pathways. Computational modelling of these motion detectors has not only been providing effective solutions to artificial intelligence, but also benefiting the understanding of complicated biological visual systems. These biological mechanisms through millions of years of evolutionary development will have formed solid modules for constructing dynamic vision systems for future intelligent machines. This article reviews the computational motion perception models originating from biological research of insects' visual systems in the literature. These motion perception models or neural networks comprise the looming sensitive neuronal models of lobula giant movement detectors (LGMDs) in locusts, the translation sensitive neural systems of direction selective neurons (DSNs) in fruit flies, bees and locusts, as well as the small target motion detectors (STMDs) in dragonflies and hover flies. We also review the applications of these models to robots and vehicles. Through these modelling studies, we summarise the methodologies that generate different direction and size selectivity in motion perception. At last, we discuss about multiple systems integration and hardware realisation of these bio-inspired motion perception models

Toward an Autonomous Lunar Landing Based on Low-Speed Optic Flow Sensors

International audienceFor the last few decades, growing interest has returned to the quite chal-lenging task of the autonomous lunar landing. Soft landing of payloads on the lu-nar surface requires the development of new means of ensuring safe descent with strong final conditions and aerospace-related constraints in terms of mass, cost and computational resources. In this paper, a two-phase approach is presented: first a biomimetic method inspired from the neuronal and sensory system of flying insects is presented as a solution to perform safe lunar landing. In order to design an au-topilot relying only on optic flow (OF) and inertial measurements, an estimation method based on a two-sensor setup is introduced: these sensors allow us to accu-rately estimate the orientation of the velocity vector which is mandatory to control the lander's pitch in a quasi-optimal way with respect to the fuel consumption. Sec-ondly a new low-speed Visual Motion Sensor (VMS) inspired by insects' visual systems performing local angular 1-D speed measurements ranging from 1.5 • /s to 25 • /s and weighing only 2.8 g is presented. It was tested under free-flying outdoor conditions over various fields onboard an 80 kg unmanned helicopter. These pre-liminary results show that the optic flow measured despite the complex disturbances encountered closely matched the ground-truth optic flow

Bio-inspired motion detection in an FPGA-based smart camera module

Köhler T, Roechter F, Lindemann JP, Möller R. Bio-inspired motion detection in an FPGA-based smart camera module. Bioinspiration & Biomimetics. 2009;4(1):015008.Flying insects, despite their relatively coarse vision and tiny nervous system, are capable of carrying out elegant and fast aerial manoeuvres. Studies of the fly visual system have shown that this is accomplished by the integration of signals from a large number of elementary motion detectors (EMDs) in just a few global flow detector cells. We developed an FPGA-based smart camera module with more than 10000 single EMDs, which is closely modelled after insect motion-detection circuits with respect to overall architecture, resolution and inter-receptor spacing. Input to the EMD array is provided by a CMOS camera with a high frame rate. Designed as an adaptable solution for different engineering applications and as a testbed for biological models, the EMD detector type and parameters such as the EMD time constants, the motion-detection directions and the angle between correlated receptors are reconfigurable online. This allows a flexible and simultaneous detection of complex motion fields such as translation, rotation and looming, such that various tasks, e. g., obstacle avoidance, height/distance control or speed regulation can be performed by the same compact device

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here we present our largest increase in plant, metazoan and fungal genomes since the project’s inception creating one of the world’s most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We also detail our new efforts in gene annotation, our emerging support for pangenome analysis and efforts to accelerate data dissemination through the Ensembl Rapid Release resource. We also present our new AlphaFold visualisation. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl’s release cycle

Ensembl 2014

Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training

CADD: predicting the deleteriousness of variants throughout the human genome

Combined Annotation-Dependent Depletion (CADD) is a widely used measure of variant deleteriousness that can effectively prioritize causal variants in genetic analyses, particularly highly penetrant contributors to severe Mendelian disorders. CADD is an integrative annotation built from more than 60 genomic features, and can score human single nucleotide variants and short insertion and deletions anywhere in the reference assembly. CADD uses a machine learning model trained on a binary distinction between simulated de novo variants and variants that have arisen and become fixed in human populations since the split between humans and chimpanzees; the former are free of selective pressure and may thus include both neutral and deleterious alleles, while the latter are overwhelmingly neutral (or, at most, weakly deleterious) by virtue of having survived millions of years of purifying selection. Here we review the latest updates to CADD, including the most recent version, 1.4, which supports the human genome build GRCh38. We also present updates to our website that include simplified variant lookup, extended documentation, an Application Program Interface and improved mechanisms for integrating CADD scores into other tools or applications. CADD scores, software and documentation are available at https://cadd.gs.washington.edu

Ensembl 2011

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types