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Outreach and Software Development for the Apollo Genome Annotation Editor


Projects Apollo, JBrowse
Lead

Ian Holmes (University of California, Berkeley)

Funding Cycle 1

Proposal Summary

To hire an outreach coordinator and (part of) a software developer for the Apollo genome annotation editor, provide developer- and user-oriented workshops and training, develop a plugin framework, and integrate protein visualizations.


Project

Apollo

The Apollo genome annotation editor is a tool for the manual editing and revision of genome annotations. Improving the accuracy of genome annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Apollo uses a web-based graphical user interface based on a genome browser. Curators can drag gene models to edit their structure. It is somewhat similar to Google Docs in that edits to a gene model show up “live” in all users’ browsers. Increasingly, Apollo has been used as a crowdsourcing-style tool, aimed at expert members of a community who wish to contribute to the review and improvement of their organism’s annotations.


Key Personnel

Ian Holmes
Nathan Dunn

Project

JBrowse

JBrowse is a genome browser written entirely in JavaScript. It can be used to navigate and drill into genomic DNA sequences, hypotheses about the structure of those genomes (e.g. gene coordinates), and the primary evidence underpinning these hypotheses. JBrowse has become one of the most widely-used genome browsers, and the browser of choice for “budget” genome projects and projects outside of the small set of genetic model organisms (including many species of biotechnological interest). JBrowse is an extensible platform; its plugin repository contains over 50 plugins including Dynamix (for AI-assisted examination of genomic data and evidence) and Apollo (for collaborative web-based annotation of genome annotations), as well as many creative interactive visualizations contributed by third parties.


Key Personnel

Ian Holmes
Rob Buels