For this week’s tip of the week we’ll be looking at the Gaggle Genome Browser. As we are seeing more and more species or individuals data coming along from high-throughput sequencing projects, metagenomics data sets, and additional annotation track types coming from various projects–we’re gonna need more visualization options. Gaggle Browser provides the foundation for a new kind of visualization and interaction with the data.
The Gaggle Browser is one piece of the Gaggle components, actually. Gaggle is actually a framework that enables different enabled tools to interact with each other. If a database or program can interact with this system, it can be called a “Goose”. Some of the current Geese right now include the Browser, and Cytoscape, and other pieces. Check out the components page for additional interactors. And check out that figure that illustrates the Firegoose toolbar interacting with important web tools such as DAVID, STRING, KEGG, and so on. That will give you a sense of the goals of this project, and the possibility of extending and integrating the data types that might be useful for your projects.
For this tip, though, we’ll focus on the browser. A paper has just come out that provides a lot more background on the project–including extensive descriptions of the underlying software and connections. For end users, though, the key piece is what this can do for you–and the team’s goal was stated as this:
“Our choice to build the GGB as a desktop application was largely motivated by the need to support large user-generated datasets.”
This is crucial. We love the big browsers and the range that are out there now, and we rely on them every day. And newer ones like JBrowse are also contributing to our choices. But at every workshop we do these days someone says to us: I have this giant data set I need to look at, how can I do it? And they want to be able to more customize exactly what they want to show–for data visualization and for making figures, etc. For some people Gaggle Browser may be an answer.
In my interactions with the browser so far, I can easily see how smooth and fast the navigation around large regions can be. For my purposes I think it would be great to load up genomic regions of interest, and then add a type of annotation track I’m interested it, and then scan around. For example, I was loading up the human genome data in GGB, and then I pulled down the Transcription Factor Binding Sites (TFBS conserved) from chromosome 1 using the UCSC Table Browser. I sent that to Galaxy to convert to the GFF file format I needed, and then loaded up the TFBS on the browser to look around. I had a little trouble with the upload at first, but after we worked that out (with the help of the handy discussion group list) I was able to do what I wanted. I’d still probably go back to UCSC to do queries and other visualizations of this data–but for a quick look around at the landscape–Gaggle was a really nice option.
In this tip I’ll load up a sample data set and move around some, showing you some of the display aspects.
For my example I’m going to load up the Bacillus anthracis demo and interact with the interface a bit to help you get started. I’ll mention some of the features, but in this short movie I won’t have time to illustrate how easy it was to load up a track of my own on the human genome. But I can certainly see the advantages of the quick custom browser I could build with data of interest.
It’s a young browser, and features are still being explored and added–but I think it could be very nice for people to interact with their large data sets of interest. I’ve already offered 2 feature requests: I would like to have labels for my tracks, and I would like to be able to choose different genome assemblies. And the Gaggle Browser team was very responsive and friendly to those inquiries.
So load up a Gaggle Browser and try it out. And start to imagine ways to load your favorite data on this framework.
Gaggle Genome Browser (GGB): http://gaggle.systemsbiology.net/docs/geese/genomebrowser/
Gaggle components homepage: http://gaggle.systemsbiology.net/docs/
Bare, J., Koide, T., Reiss, D., Tenenbaum, D., & Baliga, N. (2010). Integration and visualization of systems biology data in context of the genome BMC Bioinformatics, 11 (1) DOI: 10.1186/1471-2105-11-382