Video Tip of the Week: 3D Virtual Worm (encore)
Earlier this year I did a tip on the 3D Virtual Worm browser from the OpenWorm team. At that time, there wasn’t a publication to accompany that post. And since these tools get much more visibility when the posts go to ScienceSeeker and Research Blogging I wanted to revisit this now that there is a publication for this project.
One of the things I keep harping on is how much we need better visualization for the tremendous volumes of data we are going to have. Imagine the day when we can code the series of transcription-factor binding events followed by transcription evidence as cells differentiate into neurons. I can imagine it being just amazing to watch, but also providing insights into basic processes. That was true when the Virtual Cell team recently was coding up the cellular processes. Things they saw in the model helped refine the understanding of the biology, and vice versa. Understanding the initial steps better can also help us to look for ways to enhance tissue repair potentially. We’re a long way from this now, but some teams are working their way towards these strategies. It’s interesting to see what the data requirements are, and how crucial public data sets are for these projects. And projects like modENCODE will offer some of the necessary data foundations for that for worm, and I can see ENCODE and later projects doing that for virtual tissue culture cells someday.
In this paper the describe the work that has brought them to the point we find ourselves with the virtual worm. The schematic diagrams and the subsequent worm images are really compelling to look at and consider. And to note the crucial underlying benchwork studies that enable this to happen is important. Sometimes there’s tension between the bench and the computational perspectives on projects like “virtual” cells or organisms. But there’s undoubtedly room for both.
Here’s an earlier prototype of the features of this work from this team. It gives you a better sense of the innards of the process:
Certainly we are in an early phase of the work. But it’s important to head there, and it’s nice to see people thinking through the issues and working it out. And the worm 3D browser will continue to improve as groups like this team bring their work to the project.
Load the virtual worm and take a spin: http://browser.openworm.org/
More about the OpenWorm project: https://code.google.com/p/openworm/
Palyanov, A., Khayrulin, S., Larson, S.D., & Dibert, A. (2012). Towards a virtual C. elegans: A framework for simulation and visualization of the neuromuscular system in a 3D physical environment In Silico Biology, 11 (3), 137-147 DOI: 10.3233/ISB-2012-0445