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  1. Article ; Online: Spec2Vec

    Florian Huber / Lars Ridder / Stefan Verhoeven / Jurriaan H Spaaks / Faruk Diblen / Simon Rogers / Justin J J van der Hooft

    PLoS Computational Biology, Vol 17, Iss 2, p e

    Improved mass spectral similarity scoring through learning of structural relationships.

    2021  Volume 1008724

    Abstract: Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity ... ...

    Abstract Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity scores and the true structural similarities have been described, little development of alternative scores has been undertaken. Here, we introduce Spec2Vec, a novel spectral similarity score inspired by a natural language processing algorithm-Word2Vec. Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities. Using data derived from GNPS MS/MS libraries including spectra for nearly 13,000 unique molecules, we show how Spec2Vec scores correlate better with structural similarity than cosine-based scores. We demonstrate the advantages of Spec2Vec in library matching and molecular networking. Spec2Vec is computationally more scalable allowing structural analogue searches in large databases within seconds.
    Keywords Biology (General) ; QH301-705.5
    Subject code 006
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: sv-callers

    Arnold Kuzniar / Jason Maassen / Stefan Verhoeven / Luca Santuari / Carl Shneider / Wigard P. Kloosterman / Jeroen de Ridder

    PeerJ, Vol 8, p e

    a highly portable parallel workflow for structural variant detection in whole-genome sequence data

    2020  Volume 8214

    Abstract: Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases including cancer. Despite the advances in whole genome sequencing, comprehensive and accurate detection of SVs in short-read data still ... ...

    Abstract Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases including cancer. Despite the advances in whole genome sequencing, comprehensive and accurate detection of SVs in short-read data still poses some practical and computational challenges. We present sv-callers, a highly portable workflow that enables parallel execution of multiple SV detection tools, as well as provide users with example analyses of detected SV callsets in a Jupyter Notebook. This workflow supports easy deployment of software dependencies, configuration and addition of new analysis tools. Moreover, porting it to different computing systems requires minimal effort. Finally, we demonstrate the utility of the workflow by performing both somatic and germline SV analyses on different high-performance computing systems.
    Keywords Scientific workflow ; Cancer genomics ; Variant calling ; Structural variants ; High-performance computing ; Cloud computing ; Medicine ; R ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Using modular 3D digital earth applications based on point clouds for the study of complex sites

    Martinez-Rubi, Oscar / Eduardo Dias / Jisk Attema / Maarten van Meersbergen / Maurice de Kleijn / Niels Drost / Pjotr Svetachov / Rens de Hond / Rob van Nieuwpoort / Stefan Verhoeven

    International journal of digital earth. 2016 Dec. 1, v. 9, no. 12

    2016  

    Abstract: This article discusses the use of 3D technologies in digital earth applications (DEAs) to study complex sites. These are large areas containing objects with heterogeneous shapes and semantic information. The study proposes that DEAs should be modular, ... ...

    Abstract This article discusses the use of 3D technologies in digital earth applications (DEAs) to study complex sites. These are large areas containing objects with heterogeneous shapes and semantic information. The study proposes that DEAs should be modular, have multi-tier architectures, and be developed as Free and Open Source Software if possible. In DEAs requiring high reliability in the 3D measurements, point clouds are proposed as basis for the 3D Digital digital earth representation. For the development of DEAs, we propose to follow a workflow with four components: data acquisition and processing, data management, data analysis and data visualization. For every component, technological challenges of using 3D technologies are identified and solutions applied for a case study are presented. The case study is a modular 3D DEA developed for the archaeological project Mapping the Via Appia. The 3D DEA allows archaeologists to virtually analyze a complex study area.
    Keywords case studies ; computer software ; digital images ; Earth Observing System ; information management
    Language English
    Dates of publication 2016-1201
    Size p. 1135-1152.
    Publishing place Taylor & Francis
    Document type Article
    ISSN 1753-8955
    DOI 10.1080/17538947.2016.1205673
    Database NAL-Catalogue (AGRICOLA)

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