Check out the latest new release (5.3.0) of the Alliance of Genome Resources (Alliance) which includes two new species–Xenopus laevis and Xenopus tropocalis and data refreshes for many data types. The Alliance features standardized and harmonized views for data such as disease models, Gene Ontology (GO), orthology, genetic interactions and many more, for a total of 9 species including C. elegans, human and the two new frog species. Learn more about this release via the 5.3.0 Release Notes.
New Author First Pass release marks the transition to ACKnowledge!
WormBase is excited to announce that the Author First Pass project received support from the National Library of Medicine and is now officially known as ACKnowledge (Author Curation to Knowledgebase). This change reflects our commitment to expanding artificial intelligence (AI)-enhanced community curation to capture more detailed experimental findings and to introduce our curation pipeline to additional model organism communities and their respective knowledgebases.
While busy transitioning our project and enhancing our AI methods, we also implemented further improvements to the current pipeline based on continuing valuable feedback from authors. These improvements will help authors add more information about their papers and readily find previously published papers processed by our pipeline for curation using our Author Curation Portal.
A full list of enhancements is available in the V4 Release Notes.
We could have not achieved this exciting milestone without the continuous support and participation of the wonderful C. elegans community. Please continue to contribute to this important initiative!
WS286 genome browser
The new genome browser software is a live, in-page genome browser that you can add tracks to, pan, zoom and do a variety of things JBrowse 1 could do without leaving the page. If you’d like a full page JBrowse 2, you can click on the link just above the genome browser, or if you’d like to use JBrowse 1, you can click on the “Legacy” link just below JBrowse 2 to get the old JBrowse 1 image and link back. Please let us know if you have any comments or questions by writing to help@wormbase.org.
End-of-life status for GBrowse; to be retired at the end of 2022
GBrowse — the original genome browser at WormBase — has reached an end-of-life support status. Accordingly, we plan to retire GBrowse from the WormBase website at the end of 2022.
JBrowse, the successor to GBrowse, has been the primary genome browser at WormBase for many years. Recently, we released JBrowse2 which fills in the final remaining functionality gaps that existed with GBrowse.
GBrowse was a critical initial component of the Generic Model Organism Database project whose objective was to create modular software components for online genomic resources. Ahead of its time in many ways, GBrowse launched with a sophisticated plug-in mechanism that allowed it to keep pace with rapid advancements in genome sequencing, high-throughput experimental approaches and the resulting data deluge. Over the following decades, GBrowse saw numerous improvements, including the adoption of a more interactive interface, and the addition of many tools for data display, download, and analysis.
Do you have any questions or concerns about the retirement of GBrowse? Please let us know how we can help at help@wormbase.org.
International C. elegans conference 2023 website available
The 2023 International C. elegans conference is happening! Important dates to note are here. WormBase looks forward to interacting with its users and participating in many events. Watch this space for more information.