Search for either ‘WormBase’ or ‘WormBase Outreach’ in YouTube and check out our new WormBase channel, in order to view video tutorials about various types of data. These videos address commonly asked questions, like how to find a particular type of data in WormBase, or how to query WormMart for a data set. We hope to add many more tutorials in the coming days. Happy Viewing!
Would you like to browse a virtual 3D interactive atlas of the worm? Check out the ‘virtual worm’ at the Virtual Worm Project, a computer generated 3D model of the adult hermaphrodite of Caenorhabditis elegans at cellular resolution. Browse the model interactively in the 3D graphics program, Blender, or through any WebGL-enabled web browser, via the Open Worm Browser. See this page for a list of supporting browsers. The Virtual Worm site includes several ~5 minute video tutorials explaining how to use and view the model in Blender.
Currently, WormBase is using this model to generate expression pattern images based on curated expression pattern objects in the database. The Virtual Worm image can be viewed by opening the expression widget on the WormBase gene page. If the gene has post-embryonic spatial expression information, a Virtual Worm image is depicted of the cells and tissues in which it is expressed. In the future we hope to embed the browsable Virtual Worm model directly into the WormBase website, with added anatomy meta-data, as well as hyperlinks to relevant anatomy pages. We also plan on developing 3D models of embryonic and larval stages as well as the adult male. For any questions, comments, or suggestions, please contact Chris Grove at cgrove@caltech.edu.
We have been working on marking possible genome sequence errors in the C.elegans reference genome using data from the following projects:
– Weber KP et al. (2010) PLoS One “Whole genome sequencing highlights genetic changes associated with laboratory ….” (PMID 21085631)
– Doitsidou M et al. (2010) PLoS One “C. elegans mutant identification with a one-step whole-genome-sequencing and ….” (PMID 21079745)
– McGrath PT et al. (2011) Nature “Parallel evolution of domesticated Caenorhabditis species targets pheromone ….” (PMID 21849976)
This data has been used to mark regions for improvement (also available as GFF3 features), taking the total of these locations in the C. elegans database to 2,428.
We will address some of them in the next WormBase release WS234.
Update: the genome changes were deferred from WS234 to WS235