If you like building software for people to understand data better, this may be a good opportunity for you.
To apply please send your resume to Dr. Loraine via email to aloraine@charlotte.edu
Integrated Genome Browser is open source, genome visualization software scientists use to visualize and interact with genomic data. IGB is best known for fast animated zooming through a genome, visual configurability, and access to diverse data.
By working with us on the IGB project, you will gain deeper knowledge of how to build and improve complex, feature-rich software. You’ll get experience using state-of-the-art, professional programming technologies and tools – such as git, Jira, maven, AWS and more. By applying and developing your skill as a builder of tools, you’ll help expand what’s currently possible in genomics data visualization.
Preferred qualifications:
- Java programming, especially experience with OSGi and/or Spring-based applications
- Django web application framework expertise (for working with BioViz Connect, App Store, and Track Hub Facade)
- Maven build tool (java), bitbucket pipelines
- User interface design and usability
- Front end, in-browser programming (javascript, CSS)
- Team programming using git (for source code management) and Jira (for task management)
- 2+ years experience in professional software development
On-going efforts:
- IGB Java API – platform support. IGB consists of OSGi “bundles” running within a modular, OSGi run-time (Apache felix). Each bundle shares its functionality with other bundles via services and/or exported packages. In this advanced role, you’ll test, improve, and document IGB services that expose key functionality of IGB to App developers.
- IGB Apps. The IGB platform is extensible. Developers can add new features as “IGB Apps,” implemented as OSGi “bundles” (jar files) that users can down and add to IGB while it’s running, using either the IGB App Store or a within-IGB interface called App Manager. We are building and improving new and existing IGB Apps. In this project, you’ll update and maintain existing IGB Apps, and develop new ones.
- IGB App Store. Using AWS cloud resources for deployment, we built an IGB App Store for developers to distribute IGB Apps to IGB users. App Store is deployed at https://apps.bioviz.org and the App Store source code repository is at https://bitbucket.org/lorainelab/appstore. People working on this project will investigate how and whether the IGB App versioning scheme is robust to changes in the platform, such as upgrading to later versions of Java and OSGI standards. Active development has ceased, but some maintenance is required.
- BioViz Connect – linking IGB and CyVerse. CyVerse is a publicly funded network of high performance computing and storage resources. CyVerse offers access to these resources via REST APIs. We connected IGB and CyVerse using these APIs and a middleware Web site called BioViz Connect. Active development has ceased, but some maintenance is required.
- Loraine Lab infrastructure. We are using AWS, ansible and bitbucket to programmatically deploy and update our sites and support the developer team. But some of the infrastructure is still configured manually, hard to update and hard to re-deploy if needed. You’ll help design new better ways of reducing IT management drudgery through automation.
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