Ants, Bees, Genomes & Evolution @ Queen Mary University London

Performance and user centric updates to Afra's annotation editor

Written by Hiten Chowdhary, cross-posted from ([]

This is a summary of the work done during this summer as part of Google Summer of Code 2017 under the organisation Open Genome Informatics under the guidance of my mentors Yannick Wurm and Anurag Priyam.

About the project

Problem Statement: Performance and user centric improvements to Afra’s annotation editor.

Brief explanation: Gene prediction models are visually inspected and manually corrected for any mistakes. Curation of gene models is carried out on Afra, a crowdsourcing platform. Afra has two models - an annotation editor and a task processor. The annotation editor is build using JBrowse and WebApollo. This project focuses on migrating Afra to the latest JBrowse and getting a unit test suite ready to optimize the annotation editor and ease the learning curve of manual curation.

Project Summary

Before the project started, I was fairly acquainted with javascript and ruby. Initially, I got familiar with JBrowse’s codebase and understood the upgrades along with changes made in different versions. We planned to get the test suite ready before the migration of Afra takes place. With the test suite in place, the migration would take place without any hassle. One can run tests to ensure annotation editing functionality is working properly.

For migration of Afra, we took a look at JBrowse and Afra’s codebase. We examined the files added to Afra’s codebase, which exhibited the annotation editor functionality along with additional features of Afra. These differences in codebase were carried over to JBrowse as a plugin. This provided the annotation editor functionality which could be easily plugged into JBrowse or any other Genome browser.

Test Suite

Annotation editor uses Jasmine for unit tests. Jasmine was easy to setup and can be executed using a simple web server. I examined the already implemented tests for different functionalities of Afra. This provided me an insight into the processing of tests implemented in Afra. Further, I added some tests for the annotation editor functionality. These tests were:

Here is the link to my commits for the test suite.

Migrating Afra to latest JBrowse

We started building a plugin for the JBrowse to carry over the annotation editor functionality to JBrowse. This would provide Afra’s annotation edition functionality to use the latest JBrowse features, making the migration process smoother. The plugin development took place in the following steps :-

Now we had a basic plugin in place that had implemented the basic annotation editing functionality. (commit)

Now additional features of Afra had to be carried over. These feature are :-

Finally, we had successfully implemented the annotation editor of Afra as a plugin of JBrowse, along with extra features of Afra too. Further, to test whether all the annotation editing functionalities are working properly we implemented the test suite for the plugin.(commit)

August 29, 2017