This week’s video tip of the week is the next in a series. It began when I took a look at GeneFriends, and their option to output the data for use in BioLayout Express3D. So of course we had to then take a look at BioLayout. While I was exploring BioLayout, I came across Virtually Immune. This project contains intricate network diagrams of immune-system related responses which you can load into BioLayout and explore. It is a very neat way to get further in your understanding of BioLayout functions, as well as being an amazing example of how to model a key system for human health. Here is their video overview:
Virtually Immune is developing computational models of the behavior of immune system responses, in part to help reduce the use of animal models. As part of a CrackIT project challenge, they developed a model of Influenza A lifecycle and macrophage responses that you can explore to help understand the goals of the project. On their “about” page, the overall goal includes:
By enabling scientists to run in silico experiments we hope to help them to model infectious and inflammatory disease-associated processes and thereby accelerate the development of of therapeutic agents. In so doing we hope this resource will assist in the reduction and refinement of the use of animals in immunological research.
Their text-based tutorial walks you through the basic steps of building the kinds of models they have: read the literature, draw the pathway you want to represent, initialize the conditions, and then simulate with BioLayout3D. The last step–Verify–means you go back to the bench and see if your computational model predictions make sense. Hopefully refining your ideas computationally can streamline the work in the lab.
To get the best sense of the capabilities of this project, go to their Pathway Models page. From here you can load up any of the examples in BioLayout and look around. When you hover over a pathway a “Show Me” button will appear near the bottom, and clicking that will load up the data in a larger format that you can explore it. On the bottom of the new page, you can click the BioLayout button to visualize this in 3D.
If you aren’t researching immune system features, that’s fine. But it will still help you to understand how pathways relevant to your work could be modeled.
Virtually Immune: http://www.virtuallyimmune.org/
Virtually Immune tutorial: http://www.virtuallyimmune.org/tutorial/
BioLayout Express3D: http://www.biolayout.org/
[can't find one for Virtually Immune yet; will attach one if I find it in the future]
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