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
