Dr. Ann Loraine is an Associate Professor in the Department of Bioinformatics and Genomics at the University of North Carolina at Charlotte. Her lab develops computational and experimental approaches for studying how alternative splicing patterns affect gene function, focusing on environmental stress responses in plants.
Complementary to this work, they also develop a genome display software called Integrated Genome Browser (IGB, pronounced igby) useful for inspecting splicing patterns and exploring genome-scale data sets.
IGB was originally developed at Affymetrix around 2001 to support the company’s tiling array products. Funding from the ENCODE project and an R01 to Greg Helt supported it in the beginning. It was one of the first Java desktop genome browsers and was designed from the beginning to handle very large data sets. Within Affymetrix, it replaced an earlier generation Java visualization tool called the Neomorphic Annotation Station, which was developed for TIGR and the Arabidopsis genome project.
Around 2004, Affymetrix released IGB as open source software, and in 2008, Ann Loraine's group at UNC Charlotte took over supporting IGB using funding from the NSF. Since then, they have added many new features, including support for visualization of RNA-Seq, ChIP-Seq and other *seq data sets.
Dr Loraine is an active participant on Biostars and contributes under the pseudonym of Ann
Her lab also maintains a source code repository at https://bitbucket.org/lorainelab
Ann Loraine of the Integrated Genome Browser
What hardware do you use?
What is your text editor?
What software do you use for your work?
RStudio and Bioconductor tools. Integrated Genome Browser. Galaxy when I want a user-friendly interface to a tool or an easy way to share a data set. Cytoscape when I want to look at a network. Camtasia to make screencasts.
I also use services like Biostars, Dropbox, Basecamp, and Bitbucket. For the IGB project we use Atlassian products Jira and Confluence.
What do you use to create plots and charts?
Mainly R and IGB.
What do you consider the best language to do bioinformatics with?
Depends on what I'm doing. For data analysis, I mainly use R and python. Previously I used perl. For end user application development, I like Java and C.
What bioinformatics tools/software do not get enough recognition?
I’d like more people to know about Integrated Genome Browser, developed in my group. IGB is a desktop genome browser you download and run on your own computer.
IGB has dozens of great features, it’s highly interactive, and it does zooming really well. For example, when you click on something and zoom in, the thing you clicked stays in view and doesn’t zoom off the screen. In visualization jargon, that’s called “maintaining context.” It also has many tools to help you follow up on sequencing experiments, like options to run blast or or make custom data graphs. As there are so many features, we create lots of tutorials and host on-line seminars to help people get started. We are also constantly improving the user interface to make it more obvious and intuitive. I hope everyone who reads this will give IGB a try - http://www.bioviz.org. If you have questions, suggestions or support requests, please get in touch.
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