The Loraine Lab has new openings for new graduate students entering fall 2019 to join us early-to-mid October.
If you like building software and want to learn diverse technologies, this may be the ideal opportunity for you!
To apply please send your resume to Dr. Loraine via email to firstname.lastname@example.org.
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. IGB offers many diverse ways to look at data. Ease of navigation and visualization diversity put IGB in a class by itself.
Probably the best way to describe IGB is: it’s like Tableau, but for genomics.
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. By applying and developing your skill as a builder of tools, you’ll help push the boundaries of what’s currently possible in genomics data visualization.
- Java programming skill
- Maven build tool; gradle also
- User interface design and usability testing
- Web programming (JS, bootstrap, HTML, CSS – the standard things)
- Team programming using git (but we can teach you – it’s not too hard!)
- Modular programming with OSGi (Apache felix and/or karaf)
- Computer graphics
- 2+ years experience in professional software development
- 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.
- 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.
- 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. Here are some examples.
- IGB Java API – platform support. IGB actually just a collection 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 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 usability, to make it more accessible to developers and researchers alike.
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/
- IGB source code – https://bitbucket.org/
- Loraine Lab code repositories – https://bitbucket.org/lorainelab