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.

Register for the UK Worm Meeting 2023!

The upcoming UK Worm Meeting is hosted at the University of East Anglia on 13th January 2023. This one-day event will bring together researchers working with C. elegans or researchers working with other nematodes who use shared resources, technologies and expertise. The event will cover a variety of topics including ageing, developmental biology and gene regulation.

The abstract submission deadline is 9th December 2022. Please send your abstracts directly to worm.meeting@uea.ac.uk after completing your registration. When submitting your abstract, please indicate if you want to be considered for a short talk, poster presentation or both.

Registration: https://store.uea.ac.uk/conferences-and-events/faculty-of-science/bio/uk-worm-meeting

-2023 UK Worm Meeting Organizers

Two new chapters in WormBook, GENETICS

Check out these two recent WormBook chapters in the journal GENETICS:

1. “Visualizing and quantifying molecular and cellular processes in Caenorhabditis elegans using light microscopy” by Pavak Shah, Zhirong Bao and Ronen Zaidel-Bar.

2. “Mitochondrial dysfunction, aging, and the mitochondrial unfolded protein response in Caenorhabditis elegans” by Cole Haynes and Siegfried Hekimi.

2023 C. elegans Community Mentor Match program

Dear Worm Community,

The Mentor Match committee is happy to announce the roll out of the 2023 C. elegans Community Mentor Match Program! 

As a MENTOR, you can:

  • Share your knowledge and expertise to facilitate the professional growth of young C. elegansresearchers; 
  • Establish new connections with talented scientists;
  • Help foster a diverse community of worm scientists around the globe;
  • Gain exposure to broad and diverse perspectives;

For further information about the program, please see this link.

If you are willing to serve as a MENTOR, please sign up here before December 1*.

*Mentors can be postdocs, faculty members, or non-academic scientists with a C. elegansbackground.

*Note that the prospective mentor list will be made public for prospective mentees to browse.

*Please fill out the survey this year even if you have served as a mentor in the past. 

(You do not have to fill it out if you are simply maintaining an existing mentoring relationship, only if you are available for a new mentee).

Please forward this email to anyone who may not be on the WormBase email list! We would particularly like to reach former worm folks who are NOT currently in academia and may be interested in acting as a mentor for worm people considering non-academic career paths.

 A MENTEE survey will be announced via WormBase in December, as soon as the prospective mentors are in place. Stay tuned!

With best wishes,

-The C. elegans Community Mentor Match committee for 2022-23.

Meera Sundaram 
Andrea Calixto Mohor
Heather Bennett
Brent Derry
Jon Hibshman
Massimo Hilliard
Sandhya Koushika
Jeff Medley
Dan Shaye
Sander van den Heuvel

Two new species join the Alliance of Genome Resources!

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!