Browsing by Author "Lose, Thoba"

Now showing 1 - 4 of 4
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    The combat-tb workbench: Making powerful Mycobacterium tuberculosis bioinformatics accessible
    (American Society for Microbiology, 2022) van Heusden, Peter; Mashologu, Ziphozakhe; Lose, Thoba
    Whole-genome sequencing (WGS) is a powerful method for detecting drug resistance, genetic diversity, and transmission dynamics of Mycobacterium tuberculosis. Implementation of WGS in public health microbiology laboratories is impeded by a lack of user-friendly, automated, and semiautomated pipelines. We present the COMBAT-TB Workbench, a modular, easy-to-install application that provides a web-based environment for Mycobacterium tuberculosis bioinformatics. The COMBAT-TB Workbench is built using two main software components: the IRIDA platform for its web-based user interface and data management capabilities and the Galaxy bioinformatics workflow platform for workflow execution.
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    COMBAT-TB-NeoDB: Fostering tuberculosis research through integrative analysis using graph database technologies
    (Oxford University Press, 2020) Lose, Thoba; van Heusden, Peter A.; Christoffels, Alan G.
    Tuberculosis (TB) is a significant global health threat, with onethird of the population infected with its causative agent Mycobacterium tuberculosis (M.tb). Globally, researchers have been responding with a plethora of heterogeneous TB databases with each focusing on different subsets of TB data and present limited options for data integration thus impeding the chances of integrative analysis. Although each database can provide answers to certain questions in its scope, it falls short in answering questions that require federated queries across multiple domains of biological knowledge.
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    Understanding biobanking : An assessment of the public engagement speaking book intervention Biobanking and Me
    (South African Medical Association, 2019) Bedeker, Anja; Anderson, Dominique; Lose, Thoba
    Meaningful engagement with donors of biological samples intended for human-sample biobanking increases knowledge, and allows donors to make informed decisions. Informed donors provide a platform for public awareness, allowing communities to understand the impact of research, and may even encourage more people to donate biological samples. The Biobanking and Me speaking book was written to explain relevant concepts, including biobanks, genetic research and participant rights, to persons from any educational level or background. Two bilingual versions of the speaking book (English-Afrikaans and English-isiXhosa) were produced, and the impact of the speaking book was assessed.
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    Understanding M. tuberculosis variants using Galaxy and the COMBAT TB Explorer
    (Universty of the Western Cape, 2018) Lose, Thoba