Integrated Genome Browser is open source, genome visualization software used by thousands of scientists worldwide to visualize and interact with genomic data. IGB is best known for implementing fast animated zooming through a genome. It also offers many diverse ways to look at data. Ease of navigation and visualization diversity put IGB in a class by itself.

By working with us on the IGB project, you will gain deeper knowledge of how to build and improve large software systems. You’ll also get more practice using state-of-the-art, professional programming technologies and tools – such as git, Jira, maven, AWS, and more. 

Preferred requirements:

On-going efforts:

• IGB App Store. Using AWS cloud resources for deployment, we are building an IGB App Store for developers to distribute IGB Apps to IGB users. For this project, we’re are building on the code base of the Cytoscape App Store. (Cytoscape is a Java desktop client with similar architecture to IGB.) See our work-in-progress App Store source code repository at https://bitbucket.org/lorainelab/appstore.

• Linking IGB and CyVerse.CyVerse is a large, publicly funded ecosystem of HPC and storage resources. CyVerse offers access to these resource via REST APIs. We are connecting IGB and CyVerse using these APIs. When finished, this novel connectivity will empower users to run sophisticated visual analytics programs from the desktop, using IGB. They will also be able to share and publish their data on-line, using CyVerse and IGB’s simple Quickload protocol. In this project, you’ll learn about using and building on cloud-based resources, how to design and use REST APIs, and how to build Javascript interfaces to same.

• IGB Apps. We are building and improving new and existing IGB Apps. IGB Apps are nothing but jar files with OSGi-specific metadata that enables them to be dynamically loaded into IGB as OSGi bundles. IGB Apps developed by Loraine Lab provide useful new functionality to users, but also demonstrate the platform. In this project, you’ll develop new demo IGB Apps, and document same.

• IGB Java API. IGB actually just a collection of OSGi “bundles” running within a modular, OSGi run-time (Apache felix). Each bundle offers new functionality to the other bundles via services and/or exported packages. In this advanced role, you’ll develop IGB services that expose key functionality of IGB to App developers. You’ll also help improve all aspects of the platform, from build system to deployment, to make it more accessible to developers.

• AI for the user experience. This project aims to improve usability by predicting what users want to do next. In this project, you’ll use machine learning to engineer Web services that can guess parameters and settings so that users don’t have to.

For more information, see:

• On-line class on developing IGB – https://canvas.instructure.com/courses/1164217
• IGB download site – https://bioviz.org
• IGB YouTube Channel with videos showing IGB in action – https://www.youtube.com/channel/UC0DA2d3YdbQ55ljkRKHRBkg
• IGB source code – https://bitbucket.org/lorainelab/integrated-genome-browser
• Loraine Lab code repositories – https://bitbucket.org/lorainelab