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

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 Comparative genomics reveals new functional insights in uncultured MAST species

2021 ◽  
Author(s):  
Aurelie Labarre ◽  
David López-Escardó ◽  
Francisco Latorre ◽  
Guy Leonard ◽  
François Bucchini ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Genomic Data ◽  
Proton Pumps ◽  
Functional Annotations ◽  
The Core ◽  
Unicellular Eukaryotes ◽  
Microbial Eukaryotes ◽  
Core Energy ◽  
Marine Surface ◽  
Environmental Sequences

AbstractHeterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.

scholarly journals Systematizing Genome Privacy Research: A Privacy-Enhancing Technologies Perspective

2019 ◽  
Vol 2019 (1) ◽  
pp. 87-107 ◽  
Author(s):  
Alexandros Mittos ◽  
Bradley Malin ◽  
Emiliano De Cristofaro
Keyword(s):  
Data Privacy ◽  
Online Survey ◽  
Current Knowledge ◽  
Genomic Data ◽  
Well Being ◽  
Security And Privacy ◽  
Genome Data ◽  
Privacy Enhancing Technologies ◽  
Cost Efficient ◽  
New Research

Abstract Rapid advances in human genomics are enabling researchers to gain a better understanding of the role of the genome in our health and well-being, stimulating hope for more effective and cost efficient healthcare. However, this also prompts a number of security and privacy concerns stemming from the distinctive characteristics of genomic data. To address them, a new research community has emerged and produced a large number of publications and initiatives. In this paper, we rely on a structured methodology to contextualize and provide a critical analysis of the current knowledge on privacy-enhancing technologies used for testing, storing, and sharing genomic data, using a representative sample of the work published in the past decade. We identify and discuss limitations, technical challenges, and issues faced by the community, focusing in particular on those that are inherently tied to the nature of the problem and are harder for the community alone to address. Finally, we report on the importance and difficulty of the identified challenges based on an online survey of genome data privacy experts.

scholarly journals An integrated system for data quality and conditions assessment for the ATLAS Tile Calorimeter

2019 ◽  
Vol 214 ◽  
pp. 01030
Author(s):  
Juraj Smiesko
Keyword(s):  
Data Quality ◽  
Quality Assessment ◽  
Virtual Machine ◽  
Web Applications ◽  
Web Server ◽  
Integrated System ◽  
Assessment Tools ◽  
Web Interface ◽  
Data Quality Assessment ◽  
Quality Tools

An integrated system for data quality and conditions assessment for the ATLAS Tile Calorimeter is known amongst the ATLAS Tile Calorimeter as the Tile-in-One. It is a platform for combining all of the ATLAS Tile Calorimeter offline data quality tools in one unified web interface. It achieves this by using simple main web server to serve as central hub and group of small web applications called plugins, which provide the data quality assessment tools. Every plugin runs in its own virtual machine in order to prevent interference between the plugins and also to increase stability of the platform.

scholarly journals OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

2019 ◽  
Vol 47 (W1) ◽  
pp. W52-W58 ◽  
Author(s):  
Ling Xu ◽  
Zhaobin Dong ◽  
Lu Fang ◽  
Yongjiang Luo ◽  
Zhaoyuan Wei ◽  
...  
Keyword(s):  
Web Server ◽  
Venn Diagram ◽  
Orthologous Group ◽  
Genome Comparison ◽  
Species Number ◽  
Whole Genome ◽  
Functional Annotations ◽  
Occurrence Pattern ◽  
Multiple Species ◽  
User Friendly

Abstract OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to 12 species. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoa, protists, fungi, plants and bacteria, have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net.

scholarly journals Education in the genomics era: Generating high-quality genome assemblies in university courses

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Stefan Prost ◽  
Sven Winter ◽  
Jordi De Raad ◽  
Raphael T F Coimbra ◽  
Magnus Wolf ◽  
...  
Keyword(s):  
Low Cost ◽  
Genomic Data ◽  
Master's Level ◽  
Genome Data ◽  
Sequencing Technologies ◽  
Third Generation Sequencing ◽  
University Courses ◽  
Hands On ◽  
Genome Assemblies ◽  
High Quality Genome

Abstract Recent advances in genome sequencing technologies have simplified the generation of genome data and reduced the costs for genome assemblies, even for complex genomes like those of vertebrates. More practically oriented genomic courses can prepare university students for the increasing importance of genomic data used in biological and medical research. Low-cost third-generation sequencing technology, along with publicly available data, can be used to teach students how to process genomic data, assemble full chromosome-level genomes, and publish the results in peer-reviewed journals, or preprint servers. Here we outline experiences gained from 2 master's-level courses and discuss practical considerations for teaching hands-on genome assembly courses.

scholarly journals Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons

2021 ◽  
Vol 2021 (3) ◽  
pp. 28-48
Author(s):  
Kerem Ayoz ◽  
Erman Ayday ◽  
A. Ercument Cicek
Keyword(s):  
Data Sharing ◽  
Scientific Progress ◽  
Genomic Data ◽  
Substantial Part ◽  
Genome Reconstruction ◽  
Eye Color ◽  
Genome Data ◽  
Hair Type ◽  
Major Bottleneck ◽  
Inference Attacks

Abstract Sharing genome data in a privacy-preserving way stands as a major bottleneck in front of the scientific progress promised by the big data era in genomics. A community-driven protocol named genomic data-sharing beacon protocol has been widely adopted for sharing genomic data. The system aims to provide a secure, easy to implement, and standardized interface for data sharing by only allowing yes/no queries on the presence of specific alleles in the dataset. However, beacon protocol was recently shown to be vulnerable against membership inference attacks. In this paper, we show that privacy threats against genomic data sharing beacons are not limited to membership inference. We identify and analyze a novel vulnerability of genomic data-sharing beacons: genome reconstruction. We show that it is possible to successfully reconstruct a substantial part of the genome of a victim when the attacker knows the victim has been added to the beacon in a recent update. In particular, we show how an attacker can use the inherent correlations in the genome and clustering techniques to run such an attack in an efficient and accurate way. We also show that even if multiple individuals are added to the beacon during the same update, it is possible to identify the victim’s genome with high confidence using traits that are easily accessible by the attacker (e.g., eye color or hair type). Moreover, we show how a reconstructed genome using a beacon that is not associated with a sensitive phenotype can be used for membership inference attacks to beacons with sensitive phenotypes (e.g., HIV+). The outcome of this work will guide beacon operators on when and how to update the content of the beacon and help them (along with the beacon participants) make informed decisions.

scholarly journals Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method

2017 ◽  
Author(s):  
Raúl Amado Cattáneo ◽  
Luis Diambra ◽  
Andrés Norman McCarthy
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Low Frequency ◽  
Genomic Data ◽  
Data Sets ◽  
High Coverage ◽  
Genome Data ◽  
Sequencing Technologies ◽  
Alignment Free ◽  
Chloroplast Phylogeny

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filter out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.

scholarly journals CSVS, a crowdsourcing database of the Spanish population genetic variability

2020 ◽  
Vol 49 (D1) ◽  
pp. D1130-D1137 ◽  
Author(s):  
María Peña-Chilet ◽  
Gema Roldán ◽  
Javier Perez-Florido ◽  
Francisco M Ortuño ◽  
Rosario Carmona ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Population Studies ◽  
Local Population ◽  
Genomic Data ◽  
Critical Factor ◽  
Spanish Population ◽  
Web Interface ◽  
Sequencing Data ◽  
Local Variability

Abstract The knowledge of the genetic variability of the local population is of utmost importance in personalized medicine and has been revealed as a critical factor for the discovery of new disease variants. Here, we present the Collaborative Spanish Variability Server (CSVS), which currently contains more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated in a collaborative crowdsourcing effort collecting sequencing data produced by local genomic projects and for other purposes. Sequences have been grouped by ICD10 upper categories. A web interface allows querying the database removing one or more ICD10 categories. In this way, aggregated counts of allele frequencies of the pseudo-control Spanish population can be obtained for diseases belonging to the category removed. Interestingly, in addition to pseudo-control studies, some population studies can be made, as, for example, prevalence of pharmacogenomic variants, etc. In addition, this genomic data has been used to define the first Spanish Genome Reference Panel (SGRP1.0) for imputation. This is the first local repository of variability entirely produced by a crowdsourcing effort and constitutes an example for future initiatives to characterize local variability worldwide. CSVS is also part of the GA4GH Beacon network. CSVS can be accessed at: http://csvs.babelomics.org/.

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