Aviator: a web service for monitoring the availability of web services

Fehlmann, Tobias; Kern, Fabian; Hirsch, Pascal; Steinhaus, Robin; Seelow, Dominik; Keller, Andreas

doi:10.1093/nar/gkab396

Cited by 3 publications

(1 citation statement)

References 31 publications

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“…We collected 17 resources with a focus on their availability and SARS-CoV-2 relevance using Aviator [11], a tool for monitoring web services based on literature, OverCOVID (http://bis.zju.edu.cn/overcovid/resource.html), and our experience in daily work in SARS-CoV-2 surveillance. We excluded all non-molecular surveillance tools and non-working tools (although still online), resulting in this selection: GESS [12], Global evolution of SARS-CoV-2 [13], EMBL-EBI COVID-19 Data Portal [4], GISAID CoVSurver [6], CovidPhy [14], Coronavirus3D, NCBI, PathogenWatch, Nextstrain [8], CoV-GLUE [15], Outbreak, coVariants, CoV-Spectrum [10], COG-UK Mutation Explorer, COVID-19 variant dashboard, CoVerage, and Monitor of SARS-CoV-2 variants (Table S1).…”

Section: Resultsmentioning

confidence: 99%

CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance

Wittig

Miranda

Tang

et al. 2021

Preprint

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The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of molecular surveillance to understand the evolution of the virus and to monitor and plan the epidemiological responses. Quick analysis, easy visualization and convenient filtering of the latest viral sequences are essential for this purpose. We present CovRadar, a tool for molecular surveillance of the Corona spike protein. The spike protein contains the receptor binding domain (RBD) that is used as a target for most vaccine candidates. CovRadar consists of a workflow pipeline and a web application that enable the analysis and visualization of over 250,000 sequences. First, CovRadar extracts the regions of interest using local alignment, then builds a multiple sequence alignment, infers variants, consensus sequences and phylogenetic trees and finally presents the results in an interactive PDF-like app, making reporting fast, easy and flexible. CovRadar is freely accessible at https://covradar.net, its open-source code is available at https://gitlab.com/dacs-hpi/covradar.

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Section: Resultsmentioning

confidence: 99%

CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance

Wittig

Miranda

Tang

et al. 2021

Preprint

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Variant interpretation in molecular autopsy: a useful dilemma

et al. 2022

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Sudden cardiac death (SCD) in adolescents and young adults may be the first manifestation of an inherited arrhythmic syndrome. Thus identification of a genetic origin in sudden death cases deemed inconclusive after a comprehensive autopsy and may help to reduce the risk of lethal episodes in the remaining family. Using next-generation sequencing (NGS), a large number of variants of unknown significance (VUS) are detected. In the majority of cases, there is insufficient evidence of pathogenicity, representing a huge dilemma in current genetic investigations. Misinterpretation of such variants may lead to inaccurate genetic diagnoses and/or the adoption of unnecessary and/or inappropriate therapeutic approaches. In our study, we applied current (ACMG) recommendations for variant classification in post-mortem genetic screening of a cohort of 56 SCD victims. We identified a total 53 rare protein-altering variants (MAF < 0.2%) classified as VUS or worse. Twelve percent of the cases exhibited a clinically actionable variant (pathogenic, likely pathogenic or VUS – potentially pathogenic) that would warrant cascade genetic screening in relatives. Most of the variants detected by means of the post-mortem genetic investigations were VUS. Thus, genetic testing by itself might be fairly meaningless without supporting background data. This data reinforces the need for an experienced multidisciplinary team for obtaining reliable and accountable interpretations of variant significance for elucidating potential causes for SCDs in the young. This enables the early identification of relatives at risk or excludes family members as genetic carriers. Also, development of adequate forensic guidelines to enable appropriate interpretation of rare genetic variants is fundamental.

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MaterialsAtlas.org: a materials informatics web app platform for materials discovery and survey of state-of-the-art

Stanislav²,

Song³

et al. 2022

npj Comput Mater

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The availability and easy access of large-scale experimental and computational materials data have enabled the emergence of accelerated development of algorithms and models for materials property prediction, structure prediction, and generative design of materials. However, the lack of user-friendly materials informatics web servers has severely constrained the wide adoption of such tools in the daily practice of materials screening, tinkering, and design space exploration by materials scientists. Herein we first survey current materials informatics web apps and then propose and develop MaterialsAtlas.org, a web-based materials informatics toolbox for materials discovery, which includes a variety of routinely needed tools for exploratory materials discovery, including material’s composition and structure validity check (e.g. charge neutrality, electronegativity balance, dynamic stability, Pauling rules), materials property prediction (e.g. band gap, elastic moduli, hardness, and thermal conductivity), search for hypothetical materials, and utility tools. These user-friendly tools can be freely accessed at http://www.materialsatlas.org. We argue that such materials informatics apps should be widely developed by the community to speed up materials discovery processes.

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Aviator: a web service for monitoring the availability of web services

Cited by 3 publications

References 31 publications

CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance

CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance

Variant interpretation in molecular autopsy: a useful dilemma

MaterialsAtlas.org: a materials informatics web app platform for materials discovery and survey of state-of-the-art

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