Abstract
BackgroundThe complexity of genome informatics is a recurring challenge for genome exploration and analysis by students and other non-experts. This complexity creates a barrier to wider implementation of experiential genomics education, even in settings with substantial computational resources and expertise. Reducing the need for specialized software tools will increase access to hands-on genomics pedagogy.ResultsMySeq is a React.js single-page web application for privacy-protecting interactive personal genome analysis. All analyses are performed entirely in the user’s web browser eliminating the need to install and use specialized software tools or to upload sensitive data to an external web service. MySeq leverages Tabix-indexing to efficiently query whole genome-scale variant call format (VCF) files stored locally or available remotely via HTTP(s) without loading the entire file. MySeq currently implements variant querying and annotation, physical trait prediction, pharmacogenomic, polygenic disease risk and ancestry analyses to provide representative pedagogical examples; and can be readily extended with new analysis or visualization components.ConclusionsMySeq supports multiple pedagogical approaches including independent exploration and interactive online tutorials. MySeq has been successfully employed in an undergraduate human genome analysis course where it reduced the barriers-to-entry for hands-on human genome analysis.
Highlights
The complexity of genome informatics is a recurring challenge for genome exploration and analysis by students and other non-experts
We present MySeq, a freely available open-source web application, inspired by GENOtation, DNA Compass and the iobio suite, which is designed to meet the unique needs of experiential genomics pedagogy, including students analyzing their own genomic data
Creating sustainable genomics pedagogy that can be used in many different educational settings, including those with fewer resources, will require minimizing the need for specialized software and other computational infrastructure [44]
Summary
The complexity of genome informatics, and the extensive use of command-line software tools, creates barriers to the wider adoption of experiential genomics education. Students completed instructor-created laboratory exercises, e.g. predicting ABO blood group or comparing polygenic disease risk for parents and children, using the relevant scientific literature and links to specific variant queries or other MySeq analyses. These links, or even the MySeq application itself, can be embedded into another webpage to create online demos. The flexibility and ease-of-use of “client side” web applications make this an attractive approach for expanding access to experiential genomics education By supporting both locally stored and remotely available VCF files from within a browser-based tool, MySeq can take advantage of the ease-of-use of a web application while ensuring users can maintain control of their data by only storing it locally. MySeq does not provide additional encryption beyond that employed by the user and is not a substitute for implementing data security best practices, such as local data encryption
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