Service status: Enrichment, ontology browser and graph display tools are now working at WormBase
Enrichment, ontology browser and graph display tools are all working again. Thank-you for your patience. (Source: WormBase)
Source: WormBase - July 23, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news service status Source Type: news

Enrichment, ontology browser and graph display tools temporarily down at WormBase
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. (Source: WormBase)
Source: WormBase - July 19, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news service status service outtage Source Type: news

Promoting equity in the C. elegans community
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 ...
Source: WormBase - July 18, 2020 Category: Genetics & Stem Cells Authors: The WormBoard Tags: news wormboard Source Type: news

New Chapter in WormBook, GENETICS
Check out the new chapter in WormBook, GENETICS: mRNA Editing, Processing and Quality Control in Caenorhabditis elegans by Joshua Arribere, Hidehito Kuroyanagi and Heather Hundley. (Source: WormBase)
Source: WormBase - July 9, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest wormbook Source Type: news

WormBase updates in WS277 – new protein schematic images!
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, on...
Source: WormBase - July 3, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new datasets new features news release notes data release new release WS277 Source Type: news

Alliance of Genome Resources 3.1 released
The Alliance of Genome Resources is a portal for data related to six of the major model organisms and human data. The Alliance has been updated to the 3.0.1 release and contains new features and new data. Key new features include a refined home page and an allele page that includes transgenic alleles and shows variant consequences for transcripts. The Alliance also provides a Java API for access to the data. For a complete list of 3.0.1 features please see the release notes. (Source: WormBase)
Source: WormBase - July 1, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news release notes Alliance of Genome Resources Source Type: news

WormBase updated to WS276
A new release of WormBase, WS276 is live on the website. Please see the release notes which contain complete information about this release. Note that C. elegans gene descriptions in the “Overview” section of gene pages have improved orthology statements to human genes. WormBase uses the DIOPT orthology data from the Alliance of Genome Resources and has increased stringency by displaying only those human orthologs that have been determined by three or more methods. This should significantly improve the orthology data in WormBase which is also reflected in the gene descriptions.  ...
Source: WormBase - June 20, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news release notes Uncategorized new release WS276 Source Type: news

microPublication Biology is now indexed in PubMed
WormBase is happy to announce that the microPublication Biology journal is now fully listed in PubMed! To make articles easier to cite and discover, every microPublication now receives a PubMed ID, a PubMed Central ID, and a DOI. If you have published with us in the past, consider updating your citations. Indexing is retroactive for all past articles. You can see microPublications in PubMed by browsing the full index at PubMed Central. Or look for microPublications during normal searches at PubMed or PubMed Central. We look forward to receiving more submissions! (Source: WormBase)
Source: WormBase - June 19, 2020 Category: Genetics & Stem Cells Authors: Todd Harris Tags: news Uncategorized micropublication Source Type: news

Check out Venn diagrams for interaction data in WormBase
WormBase curates four different types of gene-to-gene interaction data: genetic, regulatory, physical, and predicted. These data are found in the interactions widget in each gene page. Aside from the predicted interactions, the other three types are curated with direct experimental evidence from the literature. Check out the micropublication which describes the Vennter tool. This tool is integrated into the interactions widget on WormBase gene pages and allows the visualization and analyses of interaction data. (Source: WormBase)
Source: WormBase - May 29, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news paper of interest interactions micropublication tools Source Type: news

Textpresso for coronovirus
Announcing the special edition of Textpresso covering coronavirus literature– it contains 31,000 articles from the PMC open access archive. (Source: WormBase)
Source: WormBase - May 15, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news text mining Textpresso Source Type: news

Model Organism research data related to COVID-19 at the Alliance
The Alliance of Genome Resources has been updated to the 3.0.1 release with a new resource for COVID-19 relevant model organism research data. Check it out! (Source: WormBase)
Source: WormBase - May 14, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news Alliance of Genome Resources Source Type: news

Open Publishing Fest
microPublication will participate in the Open Publishing Fest organized by  the Collaborative Knowledge Foundation. We will host four events or ‘tents’ which will focus on different aspects of microPublication and its role in scholarly communication. Mark your calendar for the following events and keep an eye on the  festival website for conference channels details! Tent 1: microPublication: A Welcome Alternative in Scholarly Communication – May 20th, 10am Pacific Join us for an hour packed of fun to learn how microPublication is shaping the future of scholarly communication! microPub...
Source: WormBase - May 11, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news meetings Uncategorized micropublication Source Type: news

Coming orthology data changes in WormBase WS276
Many of you have written to us in the past and pointed out some spurious human orthology calls for elegans genes, most of these have been noticed in the gene descriptions that appear in the Overview widget on the gene page. WormBase now uses the DIOPT orthology data from the Alliance of Genome Resources and has increased stringency by displaying only those human orthologs that have been determined by three or more methods. This should significantly improve the orthology data in WormBase which is reflected in the gene descriptions. Note that this change will go live in the WS276 version of WormBase coming soon (late April, ...
Source: WormBase - April 22, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Uncategorized orthologs WS276 Source Type: news

Alliance of Genome Resources updated
The Alliance (alliancegenome.org) 3.0 version released yesterday, has new features and new data related to the use of model organisms in understanding the genetic and genomic basis of human biology, health and disease. Salient features of the 3.0 release include new allele pages with variant and transcript data, new disease models on gene and disease pages, data files available for download, etc. To learn more about the latest features and data, check out the release notes. (Source: WormBase)
Source: WormBase - April 9, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news Alliance of Genome Resources new release Source Type: news

Still have time on your hands? Submit data via our ‘Submit Data’ page
You can submit various types of data via our data specific forms found here. The ‘Submit Data’ button is also prominently displayed on our menu bar on the home page on the left hand side. Click on this to be taken to the various data submission forms. (Source: WormBase)
Source: WormBase - March 27, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Source Type: news

Extra time on your hands? Help WormBase curate phenotypes
WormBase is doing a big push to address the backlog of phenotype curation. Please use our phenotype data submission form to submit phenotype data. Note that you can still submit phenotype data from published papers even if you are not an author on these papers. (Source: WormBase)
Source: WormBase - March 26, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news Source Type: news

C. elegans and related meeting changes
Meetings related to C. elegans and other topics have been postponed, moved to virtual spaces or cancelled due to the ongoing COVID-19 outbreak. Look in our Meetings widgets on the home page to find information about plans for these meetings. (Source: WormBase)
Source: WormBase - March 26, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community meetings news Source Type: news

Under stay at home? Consider submitting a microPublication.
Lab or university closed? Under at stay at home directive, doing your part to help slow the rate and spread of Covid-19? Need a diversion and a break from the news? Consider drafting and submitting a microPublication. microPublications are brief, single experiment peer-reviewed publications. You can also sign up to become a microPublication reviewer. (Source: WormBase)
Source: WormBase - March 25, 2020 Category: Genetics & Stem Cells Authors: Todd Harris Tags: Uncategorized Source Type: news

The difference between expression pattern and expression cluster data in WormBase
Chris Grove explains how expression pattern data differs from expression cluster data in WormBase: It’s important to understand that we have two avenues of gene expression curation at WormBase: one for individual gene expression pattern evaluation (e.g. using expression reporters like GFP or by performing an in situ hybridization of mRNA) which get captured in our “Expression Pattern” database objects (the “Expr_pattern” class) and a second avenue for larger scale (e.g. genome-wide) analyses of gene expression (e.g. RNA-Seq or microarray analyses) under certain conditions or in certain cell...
Source: WormBase - March 2, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news expression data Source Type: news

SimpleMine now includes protein domains
SimpleMine can now be used to obtain protein domains for a list of genes. You can select one or several attributes from a list, such as Gene ID, expression pattern, RNAi phenotype, allele phenotype, etc. Note that all attributes remain selected by default. (Source: WormBase)
Source: WormBase - February 29, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news SimpleMine tools Source Type: news

New Chapter in WormBook, GENETICS
Check out the new chapter in WormBook, GENETICS: ‘Caenorhabditis elegans Gastrulation: A Model for Understanding How Cells Polarize, Change Shape, and Journey Toward the Center of an Embryo‘ by Bob Goldstein and Jeremy Nance. (Source: WormBase)
Source: WormBase - February 11, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news paper of interest wormbook Source Type: news

Textpresso searches now available on WormBase pages
Textpresso is a powerful full text search engine for several biomedical literatures. Textpresso searches are now available on many types of pages in WormBase such as gene pages, variation/allele pages, molecule/chemical pages, etc., in the References widget. Note that you should have the ‘References’ widget open (by clicking on it) from the side bar on a gene, allele, or molecule page. Click on the ‘Textpresso’ link in ‘Find references identified by Textpresso’ at the bottom of the references to trigger a search for that entity by the Textpresso search engine. For example, clicking this ...
Source: WormBase - January 8, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news text mining Textpresso Source Type: news

WormBase version WS274 released
Please note that WormBase version WS274 was released and is the current release now live on the website. The version of the C. elegans reference genome in this release is WBcel235, included since WS235. Highlights of this release include: Isoseq data which was presented at the PacBioNorth America User Group meeting. We applied the PacBio post processing pipeline as described here. The resulting sequences are including in the transcript alignments and will be visible on the genome browser. They will also be included in our automatic transcript generation pipeline in a future release of WormBase.Improved code to gener...
Source: WormBase - January 6, 2020 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news release notes new release WS274 Source Type: news

New chapter in WormBook, GENETICS
Check out the new chapter in WormBook, GENETICS, ‘Biology of the Caenorhabditis elegans germline stem cell system‘ by Jane Hubbard and Tim Schedl. (Source: WormBase)
Source: WormBase - December 6, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest Source Type: news

Maintenance Service Interruption: Thursday, November 28, 2019.
WormBase will be unavailable for approximately one hour on Thursday, November 28, 2019 starting at 12:00 PM ET (UTC -4). We apologize in advance for the disruption and plan to have service restored as quickly as possible. (Source: WormBase)
Source: WormBase - November 26, 2019 Category: Genetics & Stem Cells Authors: Todd Harris Tags: Uncategorized Source Type: news

WS273 version of WormBase
Please note that the WS273 version of WormBase is live on our website.  The release notes for this version contain a detailed report of the various entities (eg. gene, allele) and the number of sequence and biological annotations. Some of the highlights are: C.elegans Nanopore data has been integrated and is being used to improve UTR annotation. Further work on improving our automatic transcript annotation is ongoing. This release includes a few hundred gene splits in Pristionchus pacificus predicted by the Sommer lab based on IsoSeq analysis. More will be included in future releases. (Source: WormBase)
Source: WormBase - November 22, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news release notes WS273 Source Type: news

Please cite the original papers where possible
When you write a paper, wherever possible cite the original, primary papers so the authors get credit. If you have used data amalgamated by WormBase, then please cite WormBase with the release version. (Source: WormBase)
Source: WormBase - November 21, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news Source Type: news

C. elegans meetings at the TAGC 2019
The C. elegans community is having sessions at The Allied Genetics Conference (TAGC), April 22-26, 2020 in Washington DC, organized by Martha Soto and Mike Boxem. Note that the abstract and early registration deadline is December 5. The C. elegans relevant page of the TAGC is here. (Source: WormBase)
Source: WormBase - November 13, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news meetings Source Type: news

Check out the new chapter in WormBook, GENETICS
Check out the latest chapter in WormBook, GENETICS: Developmental Plasticity and Cellular Reprogramming in Caenorhabditis elegans, by Joel Rothman and Sophie Jarriault. (Source: WormBase)
Source: WormBase - November 11, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest wormbook Source Type: news

Check out the WormBase paper in NAR
If you’d like to read about the latest developments at WormBase—literature curation efforts, features about the web interface, data mining options for users, and how WormBase as a founding member, interacts with the Alliance of Genome Resources to aid in cross-species data comparisons, check out our paper in Nucleic Acids Research. (Source: WormBase)
Source: WormBase - November 4, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication Featured Papers news paper of interest wormbase Source Type: news

C. elegans Development, Cell Biology, and Gene Expression Meeting
Dear Members of the Worm Community, We are happy to announce that registration is now open for: C. elegans Development, Cell Biology, and Gene Expression Meeting, within the larger TAGC 2020 Meeting, April 22–26, 2020. Conference website:    https://genetics-gsa.org/tagc-2020/   Location:  Washington, DC, USA (Gaylord National Resort & Convention Center)Abstract Submission Deadline*: December 5, 2019Registration Deadline:  December 5, 2019Early Discount:  December 5, 2019Submit a Workshop Proposal: by November 1, 2019Travel Award Deadline:&...
Source: WormBase - October 12, 2019 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: meetings Source Type: news

Join the CGC Team at the University of Minnesota!
Love worms and want to serve your community? Join the CGC and be instrumental in distributing C. elegans to the worldwide research community.  After 27 years of dedication to fulfilling our C. elegans needs, Theresa Stiernagle is retiring. The CGC seeks a replacement with significant worm experience (picking, scoring phenotypes, familiarity with interpreting genotypes, etc.), extreme attention to detail, and the ability to work efficiently and independently. An official job posting will be forthcoming, but in the meantime, inquiries can be made at cgc@umn.edu. (Source: WormBase)
Source: WormBase - October 11, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news positions available cgc Source Type: news

New chapter in WormBook, GENETICS
Check out the latest new chapter in WormBook, GENETICS: TOR Signaling in Caenorhabditis elegans Development, Metabolism and Aging, by T. Keith Blackwell, Aileen K. Sewell, Ziyun Wu and Min Han. (Source: WormBase)
Source: WormBase - October 11, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest wormbook Source Type: news

Call for Proposals for Undiagnosed Disease Network Gene Function Studies
The Call for Proposals for Undiagnosed Disease Network Gene Function Studies has been posted on the UDN website: https://undiagnosed.hms.harvard.edu/research/funding-opportunities/ Researchers outside of the United State can apply. (Source: WormBase)
Source: WormBase - September 22, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news grants Undiagnosed disease network Source Type: news

microPublications now indexed in Europe PMC!
microPublications are now integrated in the search, citation network, text-mining pipeline, ORCID claiming and other tools and services provided by Europe PMC. Indexing in Europe PMC increases the visibility of your microPublication, making it easier for others to find and cite your research. To learn more, visit the Europe PMC website. Thank you for supporting Open Science by sharing your data with the community! (Source: WormBase)
Source: WormBase - September 20, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news micropublication Source Type: news

New Chapter in WormBook, GENETICS
Check out the latest chapter in WormBook, GENETICS: Males, Outcrossing, and Sexual Selection in Caenorhabditis Nematodes by Asher D. Cutter, Levi T. Morran and Patrick C. Phillips. (Source: WormBase)
Source: WormBase - September 9, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news paper of interest wormbook Source Type: news

C. elegans as a model for studying human diseases
There is a growing body of literature showing that C. elegans is a great model that contributes to the study of human disease.  Recently Dr. Andy Golden alerted us to this bit of news: Check out the show ‘Diagnosis’ on Netflix by the New York Times (episode 4). There is a very rare disease caused by mutations in the human KCNMA1 gene. If you study slo-1, perhaps you can help these patients. (Source: WormBase)
Source: WormBase - September 4, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Source Type: news

New chapter in WormBook (GENETICS): The Caenorhabditis elegans Transgenic Toolbox
Check out this useful chapter ‘The Caenorhabditis elegans Transgenic Toolbox‘ by Jeremy Nance and Christian Frøkjær-Jensen in the latest issue of WormBook, GENETICS. (Source: WormBase)
Source: WormBase - August 26, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news Featured Papers paper of interest tools wormbook Source Type: news

WormBase workshop talks at the 2019 IWM available on Youtube
Talks delivered at the WormBase workshop as part of the International C. elegans meeting at UCLA in June 2019 are now available on Youtube. Please note that these are recordings done at the workshop with external cameras and microphones, so apologies if they are not of the highest quality.  They are linked from their titles below– Introduction to the WormBase webpages and widgets WormBase data mining tools: SimpleMine, WormMine, BioMart WormBase ontologies and gene set enrichment analysis WormBase JBrowse: tutorial and demo Community curation Introduction to the Alliance of Genome Resources   (Source: WormBase)
Source: WormBase - August 2, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication meetings news tutorials IWM Source Type: news

Looking for naming conventions and guidelines?
If you have started a new worm lab or are looking for nomenclature guidelines for genes, alleles and other genetic entities, please consult this page of our online user guide–https://wormbase.org/about/userguide/nomenclature#f1il048b3g6e2597cmdjkh–10 Different types of properly named entities (genes, alleles, strains, trangenes, etc.) in published papers are identified by text-mining and other WormBase tools and/or via manual curation. Following official nomenclature guidelines makes your data discoverable by WormBase and thus to the whole community! (Source: WormBase)
Source: WormBase - July 25, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news tutorials nomenclature Source Type: news

If you haven ’t signed up with WormBase, please consider doing so!
Several interactions with WormBase require that you have a WBPerson identification.  Use this form to request one, if you don’t have one already. In addition, you can also add or update your intellectual lineage. (Source: WormBase)
Source: WormBase - July 18, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news Source Type: news