WormBase has been updated to the WS225 release of the database. Please see the release notes on the WormBase Wiki.
Upgraded Forums
This weekend, we upgraded the Worm Community Forums (http://forums.wormbase.org). This upgrade includes a cleaner, simpler look-and-feel, and for us, vastly better spam protection.
New users — provided they have the smallest level of C. elegans knowledge — can register automatically without having to wait for administrator approval.
We know some things are broken. For example, some avatars may have been lost in the transition. Please let us know if you experience any odd behaviors.
Restructured FTP site
We’ve recently completed a significant restructuring of our FTP site to better accomodate additional species and third party data. We think the new structure is simple and intuitive. Some of the benefits of the new organization include:
Note: the FTP site is located at ftp.wormbase.org/pub/wormbase.
- Maintain a persistent archive of all releases:
- Download *all* the files for a given release:
A specific release:
releases/WS226/Current development release:
releases/current-dev.wormbase.org-release/Current production release:
releases/current-www.wormbase.org-release/ - Explore by species:
- Standardized file names and contents:
- Current versions of files available at standardized URLs:
- Maintain 3rd party data seamlessly side-by-side with WormBase data.
These data are available by species and abide by the same conventions mentioned above. You can process them identically to the data managed directly by WormBase.
- Standard core files; additional files of commonly requested data:
We’ve standardized the core files available for all WormBase managed species to include the genomic sequence (plain, masked, and softmasked), annotations in GFF2 or GFF3, CDS and ncRNA transcripts, and conceptual translations. We’re also expanding the number of commonly requested datasets, found in the annotations/ directory of each species:
eg: species/c_elegans/annotation
Please drop us a line if there is a file you’d like created for each WormBase release
All file names contain the species name, WormBase version, file content descriptor and appropriate file prefix. This makes processing data downloaded from WormBase simple; new files and species added to the database are easily discoverable. And if you are cherry picking data, you won’t be overwhelmed with generic “genome.tgz, genome.tgz.1, genome.tgz.2” files.
releases/WS226/species/c_elegans/c_elegans.WS226.annotations.gff2.gz
We hope these changes make it easier to find the data you are looking for.
modENCODE Data Access Webinar, May 5, 12:00 EDT
Using GBrowse and modMINE to access modENCODE data
This online webinar will familiarize its participants with the data mining tools maintained by Data Coordination Center for modENCODE – GBrowse and modMINE. This session will show how to look at modENCODE data organized as Genome Browser tracks and how to extract data of interest using query system of modMINE. Space is limited so advance registration is necessary. Please email [email protected] to reserve your spot. More details and the schedule are available on the modENCODE wiki.
Wild Isolate Entries
Wild Caenorhabditis isolate entries with geographical and ecological information are now referenced under “Strains”. To view the details of a specific wild isolate click on “Tree Display” and then “expand all nodes”. New functionalities will be available soon! To request isolates that are not stored at the CGC, please contact the “Storage Location” lab. Note that some isolate sets may be unpublished. New wild isolate data should be submitted using this online submission form.
Please send feedback to [email protected].