If you like building software and want to learn diverse technologies, this may be a good 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 many scientists use 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 combined with diversity of data available distinguish IGB from other genome browsers.
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.
Preferred requirements (software positions):
- Java programming skill
- Maven build tool; gradle also
- User interface design and usability testing (HCI expertise and training)
- Team programming using git (but we can teach you – it’s not too hard!)
- Modular programming with OSGi (Apache felix and/or karaf and/or Spring)
- Computer graphics
- 2+ years experience in professional software development
Preferred requirements (bioinformatics positions):
- Deep and up-to-date knowledge of genomics and molecular biology
- BA or BS (or higher) in a life sciences discipline; 3.5 or above overall GPA
- Basic training in how to use bioinformatics software
- Communication skills – written and verbal
- Customer service skills and/or teaching experience
- Visual analysis with IGB. We have a large need for bioinformatics students to do visual analysis of large-scale genome data sets from diverse species, mainly plants and animals. Our current greatest need is for students to assist with this new project: NSF: Genomic Analysis of heat stress tolerance during tomato pollination. You’ll use IGB to analyze splicing and gene expression data sets generated by the project. As you build expertise, you’ll lead training sessions to help colleagues and community scientists learn to use IGB to look at data.
- 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 deployed at https://apps.bioviz.org and the 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, making IGB more accessible to developers and researchers alike. Mission-critical upcoming tasks for summer include: Updating to latest versions of the felix (or possible karaf) OSGi run-time and upgrading to use the latest version of Java.
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