Enrichment, ontology browser and graph display tools are all working again. Thank-you for your patience.
A disk failure on one of our servers has brought the gene set enrichment analysis tool (TEA), the Ontology Browser (WoBr) and the graph display tool on the gene page down. We are working to restore these tools as soon as possible and apologize for any inconvenience caused. We will let the community know as soon as these are restored.
From the WormBoard:
Some of you have received this message already via the “LabHeads” or other mailing lists. We are now aware of many lab heads who are not on the list. If you are a PI and did not receive this message from the LabHeads list on July 9, please request to join the LabHeads Google Group.
This message is meant to be shared with the entire community. Please read and forward this message to everyone in your lab. If you have comments about the content of the message or the survey, please email Jane Hubbard.
The last month has highlighted the undeniable history of violence and inequity toward the Black community. We acknowledge that there is structural racism throughout society, including in science. The C. elegans International Advisory Board (aka WormBoard – you can find a list of the current WormBoard representatives here) and the international C. elegans community is committed to fighting all forms of racism and discrimination, and to promoting equity and a more inclusive scientific community.
To this end, WormBoard recently met and discussed immediate, near-term, and longer-term actions to combat racism in our community, as outlined below. Real change will require a sustained and continuous effort from the whole community. We need your help to achieve a diverse, fair, and inclusive C. elegans community that will serve as a model for science at large.
Immediate: Now – End of August
Initiative #1: C. elegans community-wide climate survey
In an anonymous survey, we ask about your experience and opinions, and we invite you to comment on several initiatives. You and all your lab members (undergraduates, graduates, postdocs, technicians, senior scientists, staff, etc.) are encouraged to respond.
Please complete the 2020 Worm Community Survey (one response per person).
Survey Response closing extended to August 10, 2020
Analysis and report will be transmitted to the community: by August 31, 2020
Current survey committee: Ahna Skop, Dana Miller, Judy Yanowitz, Brent Derry, Te-Wen Lo, Swathi Arur
Initiative #2: Worm Mentoring Match
WormBoard will develop a system to facilitate career mentoring by matching senior mentors with postdocs and junior faculty, prioritizing mentees in underrepresented groups. Those interested in participating as mentors or mentees can indicate their interest on the Worm Community Sign-Up Sheet, or by contacting Jane Hubbard, Brent Derry, or Sander van den Heuvel (current WormBoard PI/Faculty mentoring committee).
Initiative #3. Communicate resources that facilitate undergraduate (UG) research experiences
In collaboration with WormBase, we will develop a website that highlights resources provided by different societies (GSA, SDB, ASCB, SACNAS, ABRCMS), institutions, and local institutions to underrepresented UGs and host PI labs.
Please contribute to this resource, by adding information to the Resource for Undergraduate Research Experiences document or by contacting anyone on WormBoard.
Near-term: September to December 2020
Initiative #4. WormBoard membership will be diversified and expanded
We will change the board to ensure ongoing representation of our community. We will aim to include underrepresented groups, a range of institution types, and various training levels.
Longer-term: now through December 2021
Initiative #5: Make regional, topic, and international worm meeting (IWM) participation more inclusive, including new travel award initiative
We will work on making talks, sessions, and workshops more diversified, and will explore new sessions on teaching and outreach. Initiatives will be developed to showcase undergraduate research and to facilitate undergraduate, graduate, and postdoc interactions. Travel awards will be made to underrepresented students to attend meetings. Additional details will follow to the community, but we envisage collaborating with programs such as summer REU/SROP/SURP and meetings such as SACNAS and ABRCMS to identify potential awardees.
Initiative #6: Create a comprehensive and user-friendly C. elegans Community WormBase Website Portal to facilitate these and future initiatives
Portal to include jobs postings, mentor match (#2), new opportunities, speaker info, the undergraduate resources page (#3), and more.
We have released the 277th version of WormBase! As always, for a detailed report please look at the WS277 release notes.
New features: We’ve updated the protein schematic image in the homology widget on protein pages (see, for example, the UNC-2, isoform a page.) This image displays protein domains and exons mapped to amino acid coordinates, making it easy to see which regions of a transcript correspond to specific features. Driven by JBrowse — the genome browser at WormBase — users can click through the image to an interactive view in amino acid coordinates. From that familiar interface, one can scroll, export sequence (can they?), get additional information on specific features, and zoom in to single amino acid residue resolution, color-coded by chemical property. The previous static protein schematic image remains available by clicking on the “Legacy Protein Schematics” link, but will be removed after the WS278 release.
New data sets:
C. elegans: Additional Nanopore transcript data has been added.
C. elegans VC20210: The VC2010 strain data includes gene annotation which has been manually curated to improve the coding gene structures lifted over from the N2 strain annotation. This process is substantially complete, with some work still to be done on chromosome X. The number of coding genes which do not map correctly has been reduced so far from around 400 down to 50 genes which cannot yet be located and 10 which appear to be pseudogenes in VC2010. There are 20 genes which appear to be duplicated in N2 and have disappeared in VC2010. There have been 39 novel coding genes created.