My previous Video Tip of the Week highlighted the GeneFriends tool. With GeneFriends you can search for co-expression of genes in RNA-seq data sets. But you can take these results further and visualize them with the BioLayout Express3D tool, so I wanted to bring more details about BioLayout in this tip since we haven’t covered it before.
BioLayout isn’t a new tool, it’s been around for some time. The first published report of it appeared in 2001. Their publications page reflects their progress over the years, including a new paper recently put out for open peer review (very nifty, kudos on that). BioLayout keeps getting new features as it is under active development, and it keeps incorporating the key standards like BioPax that are important for interoperability of tools in this space. You can learn more about BioPax and related standards from the The ‘COmputational Modeling in BIology’ NEtwork (COMBINE) site.
This video tip will highlight their overview video to give you a taste of what BioLayout Express can do. But they have a page with more videos that can take you further on understanding and using the features of the software.
There’s a Nature Protocols paper that they produced a few years back that helped me to grasp what they want to accomplish and how to work with BioLayout. Although some of the details will have changed, I like these kinds of papers as a way to approach the concepts of working with the tools, so I’ve included that below as well. You can access it from their publications page.
BioLayout Express can handle very impressive numbers of data sets and the corresponding nodes and edges. Their publications page also offers a look at how some researchers have used their tool to advance their research. I like when tool providers offer these kinds of published examples, it helps to see how people really are using the tools.
BioLayout Express3D: http://www.biolayout.org/
Enright, A., & Ouzounis, C. (2001). BioLayout–an automatic graph layout algorithm for similarity visualization Bioinformatics, 17 (9), 853-854 DOI: 10.1093/bioinformatics/17.9.853
Theocharidis A., Stjin van Dongen, Anton J Enright & Tom C Freeman (2009). Network visualization and analysis of gene expression data using BioLayout Express3D, Nature Protocols, 4 (10) 1535-1550. DOI: http://dx.doi.org/10.1038/nprot.2009.177 *cough* access from their publications page…
Wright D.W., Tim Angus, Anton J. Enright & Tom C. Freeman (2014). Visualisation of BioPAX Networks using BioLayout Express3D, F1000Research, DOI: http://dx.doi.org/10.12688/f1000research.5499.1