scholarly journals EasyMirror and EasyImport: Simplifying the setup of a custom Ensembl database and webserver for any species

2016 ◽  
Author(s):  
Richard J Challis ◽  
Sujai Kumar ◽  
Lewis Stevens ◽  
Mark Blaxter
Keyword(s):  
Fasta File ◽  
Web Interface ◽  
Ensembl Database ◽  
Genome Data ◽  
A Genome ◽  
Genome Browsers ◽  
Set Up ◽  
A Site ◽  
Genome Projects ◽  
Modular Nature

As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool to make genome data and cross-species analyses easily accessible through a web interface and a comprehensive API. Here we introduce the EasyMirror and EasyImport pipelines to facilitate the setup and hosting of custom Ensembl genome browsers. EasyMirror (https://github.com/lepbase/easy-mirror) makes it possible to set up a mirror of any Ensembl or Ensembl Genomes (including Bacteria, Metazoa, Fungi, Plants and Protists) species in four simple steps that can be run in less than an hour on a fresh Ubuntu installation. This tool exploits the modular nature of the Ensembl codebase to allow a site to be set up with none, some or all of the data hosted locally. EasyImport (https://github.com/lepbase/easy-mirror) extends this approach to simplify the import of genomic data for any species from standard flat files into the Ensembl database schema, ready to be deployed using EasyMirror. All that is needed to get started is a genome fasta file and the gene models in GFF format. Documentation for both pipelines is available at http://easy-import.readme.io

scholarly journals GenomeHubs: Simple containerised setup of a custom Ensembl database and web server for any species

2017 ◽  
Author(s):  
Richard J Challis ◽  
Sujai Kumar ◽  
Lewis Stevens ◽  
Mark Blaxter
Keyword(s):  
Web Server ◽  
Genomic Data ◽  
Web Interface ◽  
Ensembl Database ◽  
Functional Annotations ◽  
Genome Data ◽  
Genome Browsers ◽  
Genome Projects

As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool to make genome data and cross-species analyses easily accessible through a web interface and a comprehensive API. Here we introduce GenomeHubs, which provide a containerised environment to facilitate the setup and hosting of custom Ensembl genome browsers. This simplifies mirroring of existing content and import of new genomic data into the Ensembl database schema.GenomeHubs also provide a set of analysis containers to decorate imported genomes with results of standard analyses and functional annotations and support export to flat files, including EMBL format for submission of assemblies and annotations to INSDC.Database URL: http://GenomeHubs.org

scholarly journals GenomeHubs: Simple containerised setup of a custom Ensembl database and web server for any species

2017 ◽  
Author(s):  
Richard J Challis ◽  
Sujai Kumar ◽  
Lewis Stevens ◽  
Mark Blaxter
Keyword(s):  
Web Server ◽  
Genomic Data ◽  
Web Interface ◽  
Ensembl Database ◽  
Functional Annotations ◽  
Genome Data ◽  
Genome Browsers ◽  
Genome Projects

As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool to make genome data and cross-species analyses easily accessible through a web interface and a comprehensive API. Here we introduce GenomeHubs, which provide a containerised environment to facilitate the setup and hosting of custom Ensembl genome browsers. This simplifies mirroring of existing content and import of new genomic data into the Ensembl database schema.GenomeHubs also provide a set of analysis containers to decorate imported genomes with results of standard analyses and functional annotations and support export to flat files, including EMBL format for submission of assemblies and annotations to INSDC.Database URL: http://GenomeHubs.org

Eels Under Standing Wave Conditions

1982 ◽  
Vol 40 ◽  
pp. 492-495
Author(s):  
O.L. Krivanek ◽  
J. TaftØ
Keyword(s):  
Standing Wave ◽  
Wave Conditions ◽  
Set Up ◽  
A Site ◽  
Complex Crystal

It is well known that a standing electron wavefield can be set up in a crystal such that its intensity peaks at the atomic sites or between the sites or in the case of more complex crystal, at one or another type of a site. The effect is usually referred to as channelling but this term is not entirely appropriate; by analogy with the more established particle channelling, electrons would have to be described as channelling either through the channels or through the channel walls, depending on the diffraction conditions.

scholarly journals HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Edwin A. Solares ◽  
Yuan Tao ◽  
Anthony D. Long ◽  
Brandon S. Gaut
Keyword(s):  
Cost Function ◽  
Anopheles Funestus ◽  
Hill Climbing ◽  
Optimization Approach ◽  
Sequencing Technology ◽  
Genome Data ◽  
A Genome ◽  
Long Read ◽  
Downstream Analysis ◽  
The Cost

Abstract Background Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding. Results Here we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. We illustrate the performance of HapSolo on genome data from three species: the Chardonnay grape (Vitis vinifera), with a genome of 490 Mb, a mosquito (Anopheles funestus; 200 Mb) and the Thorny Skate (Amblyraja radiata; 2650 Mb). Conclusions HapSolo rapidly identified candidate assemblies that yield improvements in assembly metrics, including decreased genome size and improved N50 scores. Contig N50 scores improved by 35%, 9% and 9% for Chardonnay, mosquito and the thorny skate, respectively, relative to unreduced primary assemblies. The benefits of HapSolo were amplified by down-stream analyses, which we illustrated by scaffolding with Hi-C data. We found, for example, that prior to the application of HapSolo, only 52% of the Chardonnay genome was captured in the largest 19 scaffolds, corresponding to the number of chromosomes. After the application of HapSolo, this value increased to ~ 84%. The improvements for the mosquito’s largest three scaffolds, representing the number of chromosomes, were from 61 to 86%, and the improvement was even more pronounced for thorny skate. We compared the scaffolding results to assemblies that were based on PurgeDups for identifying secondary contigs, with generally superior results for HapSolo.

scholarly journals Heterotypic inter-GPCR ß-arrestin coupling regulates lymphatic endothelial junctional architecture in murine lymph nodes

2018 ◽  
Author(s):  
Yu Hisano ◽  
Mari Kono ◽  
Eric Engelbrecht ◽  
Koki Kawakami ◽  
Keisuke Yanagida ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Lymph Nodes ◽  
Cross Talk ◽  
Transcriptional Activation ◽  
Endothelial Permeability ◽  
Lipid Mediator ◽  
Protein Signaling ◽  
A Genome ◽  
Sphingosine 1 Phosphate ◽  
A Site

AbstractLysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P) activate G protein-coupled receptors (GPCRs) to regulate key pathobiological processes. Here we report a novel lipid mediator GPCR cross-talk mechanism that modulates lymphatic endothelial junctional architecture in lymph nodes. LPAR1 was identified as an inducer of S1PR1/ ß-arrestin coupling from a genome-wide CRISPR/ Cas9 transcriptional activation screen. LPAR1 activation induced S1PR1 ß-arrestin recruitment while suppressing Gαi protein signaling. Lymphatic endothelial cells from cortical and medullary sinuses of lymph nodes which express LPAR1 and S1PR1, exhibit porous junctional architecture and constitutive S1PR1 coupling to ß-arrestin which was suppressed by the LPAR1 antagonist AM095. In endothelial cells, LPAR1-activation increased trans-endothelial permeability and junctional remodeling from zipper-like structures to puncta of adhesion plaques that terminate at actin-rich stress fibers with abundant intercellular gaps. Cross-talk between LPA and S1P receptors regulates complex junctional architecture of lymphatic sinus endothelial cells, a site of high lymphocyte traffic and lymph flow.

scholarly journals Effects of Malaise trap spacing on species richness and composition of terrestrial arthropod bulk samples

2020 ◽  
Author(s):  
D Steinke ◽  
TWA Braukmann ◽  
L Manerus ◽  
A Woodhouse ◽  
V Elbrecht
Keyword(s):  
Species Richness ◽  
Field Experiments ◽  
Collection Efficiency ◽  
Malaise Trap ◽  
Number Of Factors ◽  
Large Numbers ◽  
Set Up ◽  
Taxonomic Groups ◽  
A Site ◽  
Malaise Traps

AbstractThe Malaise trap has gained popularity for assessing diverse terrestrial arthropod communities because it collects large samples with modest effort. A number of factors that influence collection efficiency, placement being one of them. For instance, when designing larger biotic surveys using arrays of Malaise traps we need to know the optimal distance between individual traps that maximises observable species richness and community composition. We examined the influence of spacing between Malaise traps by metabarcoding samples from two field experiments at a site in Waterloo, Ontario, Canada. For one experiment, we used two trap pairs deployed at weekly increasing distance (3m increments from 3 to 27 m). The second experiment involved a total of 10 traps set up in a row at 3m distance intervals for three consecutive weeks.Results show that community similarity of samples decreases over distance between traps. The amount of species shared between trap pairs shows drops considerably at about 15m trap-to-trap distance. This change can be observed across all major taxonomic groups and for two different habitat types (grassland and forest). Large numbers of OTUs found only once within samples cause rather large dissimilarity between distance pairs even at close proximity. This could be caused by a large number of transient species from adjacent habitat which arrive at the trap through passive transport, as well as capture of rare taxa, which end up in different traps by chance.

NCBI submission protocol for microbial pathogen surveillance v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Maria Balkey ◽  
Robyn Randolph ◽  
Julie Haendiges ◽  
Sai Laxmi Gubbala Venkata ◽  
...  
Keyword(s):  
Active Surveillance ◽  
Genome Sequence ◽  
Large Volume ◽  
Pathogen Detection ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Web Interface ◽  
Data Submission ◽  
Set Up

PURPOSE: Step-by-step instructions for submitting pathogen whole genome sequence data to NCBI and to the NCBI Pathogen Detection portal. This protocol covers the steps needed to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. SCOPE: for use by any laboratory submitting WGS data for species under active surveillance within NCBI’s Pathogen Detection. (This includes US laboratories in GenomeTrakr, NARMS, Vet-LIRN, PulseNet, and other non-US networks and submitters). For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. This protocol covers submission using NCBI's Submission Portal web-interface. Version history: V5: Linking directly to the metadata template guidance instead of including duplicate copies of the files in this protocol. Updated screenshot for choosing the pathogen template to reflect changes at NCBI. V4: updated screenshots to reflect NCBI submission portal changes. Updated custom BioSample template.

THE ATMOSPHERIC POTENTIAL GRADIENT AT OTTAWA, CANADA

1937 ◽  
Vol 15a (8) ◽  
pp. 119-148 ◽  
Author(s):  
D. C. Rose
Keyword(s):  
Diurnal Variation ◽  
Potential Gradient ◽  
Meteorological Conditions ◽  
Fine Weather ◽  
Points Of View ◽  
Set Up ◽  
A Site

The atmospheric potential gradient was observed continuously at the National Research Laboratories at Ottawa for a year ending December 1, 1935, and at a country station about nine miles northwest of Ottawa, for four months ending November 1, 1936. The country station was set up on a site as free as possible from man-made pollution of the atmosphere. The records were studied from two points of view, the diurnal variation and disturbances in the normal fine weather value of the potential gradient. The results indicate that the diurnal variation is similar to that of other similarly situated stations. The study of disturbances in the potential gradient shows that all disturbances can be correlated with local meteorological conditions. The disturbances were for the most part associated with the stormy conditions usual at the passage of a front. The effect of city pollution on potential gradient records is clearly shown.

scholarly journals Communication as a moral vocation: Safe space and freedom of speech

2019 ◽  
Vol 68 (1) ◽  
pp. 3-16
Author(s):  
David W. Hill
Keyword(s):  
Emmanuel Levinas ◽  
Cultural Theory ◽  
Max Weber ◽  
Judith Butler ◽  
Freedom Of Speech ◽  
Safe Spaces ◽  
Liberal Democratic ◽  
Set Up ◽  
A Site ◽  
The University

The use of safe spaces in universities has become increasingly controversial over the last few years. Safe spaces are set up to offer an environment in which marginalised identities and hidden experiences can be given a voice, allowing for acceptance and affirmation. Their critics charge that they are at odds with the university as a site of debate; that their use has a chilling effect on free speech; and even that safe spaces are harmful to liberal democratic society itself. This article draws on social and cultural theory in order to counter these attacks on safe spaces. Working with Max Weber, Judith Butler and Emmanuel Levinas, the first section introduces the idea of communication as a moral vocation, calling for greater recognition of the need to balance the universal (freedom of speech) with a responsibility to hear voices that are not already amplified. Building on this, and drawing additionally on Jacques Derrida and Sara Ahmed, the second section introduces the idea of debate fetishism, which serves to negate the moral function of communication, naturalise the dominance of privileged voices, and neutralise the struggles of the struggling to be heard. It is concluded that safe spaces pose no threat to freedom of speech but that the stigmatisation of their use acts to further disadvantage underrepresented identities.

scholarly journals Recent Development of the Atomic Line List

Galaxies ◽  
2018 ◽  
Vol 6 (2) ◽  
pp. 63 ◽  
Author(s):  
Peter Van Hoof
Keyword(s):  
Transition Probabilities ◽  
Atomic Line ◽  
Spectral Features ◽  
Online Database ◽  
Web Interface ◽  
Paper Briefly ◽  
Line List ◽  
Atomic Lines ◽  
Set Up ◽  
The Web

The Atomic Line List is an online database of wavelengths and transition probabilities of atomic lines. It is primarily set up as a tool to help identify unknown spectral features. This paper briefly describes the web interface, how the line list is constructed, and what development is currently being undertaken for the next release.

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