Tag Archives: c. elegans

Video Tip of the Week: A 3D Worm!

In this era of big data and computational tools, it’s easy to generate huge amounts of texty and statistical data that offers great insights into biology, and delivers leads to design experiments in actual organisms and cells. But the cell and developmental biologist in me still yearns for great visualization tools to explore the results, beyond rows and columns and p-values. I think that better visualizations of the “-omics” data is still one of the unmet needs in this arena, and I’ve talked about that more than once but most recently here.

I’ve been keeping an eye on the progress at WormBase because I knew that they were going to be changing over to their new interface soon (it’s there now and you should see the slick new look, and that means I have to update our tutorial once it’s all stable). So I was watching their blog for updates. One of the posts they had was for a different project, though, and I was really intrigued. They were touting the OpenWorm browser, which offers a 3D representation of a worm that you can interact with. I was hooked. Heh. (Hookworm–get it? Eh, nevermind….)

So I looked into the tool a bit more. There’s no publication on the current iteration (but it is referenced in the WormBase paper below), but I was reading up on some components and I watched the several videos on the OpenWorm site that talk in more detail about the goals and the project. The very enthusiastic talk by Stephen Larson comparing the worm to Lt. Data from StarTrek was quite engaging and accessible, and a nice demonstration of public outreach for complex science.

So, it’s not Lt. WormData yet exactly. But it’s a nice effort and I can see how it could be useful for visualizing complex data as it gets layered on to the physical structures. Transcription factor binding signals. Levels of expression of RNA-seq data. Opening chromatin. Protein modifications. All kinds of important biological stuff which I usually think of as “tracks” on genome browser could definitely be represented here. I hope it expands and that we can do these sorts of things for other organisms and cells and tissues.

And quite frankly it was just fun to drive it around. Check it out. Take this worm for a spin. And really–you can spin it… It looks like the future to me.

Quick links:

OpenWorm project information: http://www.openworm.org/

OpenWorm code project page: http://code.google.com/p/openworm/

OpenWorm 3D browser: http://browser.openworm.org

WormBase Virtual worm: http://caltech.wormbase.org/virtualworm/

WormBase (new site: http://www.wormbase.org ) and (legacy site: http://legacy.wormbase.org/)

Reference for WormBase:

Yook, K., Harris, T., Bieri, T., Cabunoc, A., Chan, J., Chen, W., Davis, P., de la Cruz, N., Duong, A., Fang, R., Ganesan, U., Grove, C., Howe, K., Kadam, S., Kishore, R., Lee, R., Li, Y., Muller, H., Nakamura, C., Nash, B., Ozersky, P., Paulini, M., Raciti, D., Rangarajan, A., Schindelman, G., Shi, X., Schwarz, E., Ann Tuli, M., Van Auken, K., Wang, D., Wang, X., Williams, G., Hodgkin, J., Berriman, M., Durbin, R., Kersey, P., Spieth, J., Stein, L., & Sternberg, P. (2011). WormBase 2012: more genomes, more data, new website Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr954

New Online Tutorials on FlyBase, WormBase and Mouse Genome Informatics (MGI) Resources

Comprehensive tutorials on the model organism bioinformatics databases FlyBase, WormBase and MGI enable researchers to quickly and effectively use these invaluable resources.

OpenHelix today announced the availability of new tutorial suites on several model organism resources including FlyBase, WormBase and an update on the Mouse Genome Informatics (MGI) database. Model organisms are integral to our understanding of basic biology and modern biomedical research. Drosophila, C. elegans and mice are three highly researched model organisms. FlyBase and WormBase are the primary resources for molecular and genetic information on the Drosophilidae and on Caenorhabditis elegans and related species, respectively. MGI is a series of tools and databases that integrate genetics, genomics and biology for the laboratory mouse.

The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users to:

  • perform Quick Searches and navigate gene summary pages
  • browse genetic features within the context of the entire chromosome
  • construct complex queries across various sets of data stored within FlyBase, WormBase or MGI
  • perform nucleotide or amino acid sequence homology searches
  • output data in various formats, or access large data reports
  • investigate many related resources associated with MGI

To find out more about these and other tutorial suites visit OpenHelix.