Sir John Sulston
We mourn the passing of one of the founders of our field. John Sulston was personally responsible for establishing the use of C. elegans to study development – with his stunning determination of the entire embryonic cell lineage by direct observation – as well as obtaining a complete genome sequence. He was a mentor and role model for many of us in the field who had the opportunity to work with him or know him personally, and an inspiration for many others who only knew him through papers and oral history. He demonstrated that comprehensive and careful description can lead to fundamental, mechanistic insights into biol...
Source: WormBase - March 15, 2018 Category: Genetics & Stem Cells Authors: Todd Harris Tags: news In Memoriam Source Type: news
WormBase Release WS263
We would like to announce the availability of the WormBase WS263 release on the WormBase website and FTP.
Some of the highlights of this release are:
New Pristionchus Assembly and Gene Set
The new data made available through WormBase is described in “Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus“ by Christian Roedelsperger, et al. in Cell.
ID mapping was carried out to try and preserve the existing IDs. The published IDs were also incorporated into the database so that they are searchable on wormbase.org.
New PantherDB data
t...
Source: WormBase - March 8, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: release notes WS263 Source Type: news
New Chapter in WormBook about Sexual Dimorphism and Sex Differences
Check out the new chapter in WormBook, GENETICS: Sexual Dimorphism and Sex Differences in Caenorhabditis elegans Neuronal Development and Behavior by Maureen M. Barr, L. Rene García and Douglas S. Portman. (Source: WormBase)
Source: WormBase - March 2, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news wormbook Source Type: news
WormBase Version WS262
If you noticed, version WS262 has been out for several days. The version number present at the top of the WormBase home page is now a link to the Release Notes which is a concise summary listing the various data types and their numbers. Check it out if you want to get a quick view of the breadth and depth of the data in WormBase and to see what has changed since the last release. Also find the list of data files available for this release, on our FTP site. (Source: WormBase)
Source: WormBase - January 31, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news release notes WS262 Source Type: news
Read about repressive chromatin in new WormBook chapter
Check out the new chapter in WormBook (Genetics)–Repressive Chromatin in Caenorhabditis elegans: Establishment, Composition and Function, by Julie Ahringer and Susan M. Gasser. (Source: WormBase)
Source: WormBase - January 30, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest wormbook Source Type: news
New datatypes for Micropublication now available!
Micropublication:biology has new datatype articles! Get in touch at contact@micropublication.org and Micropublish Genetic screens, Methods, Phenotype, Genotype, and Gene Expression results or visit the Micropublication website. (Source: WormBase)
Source: WormBase - January 25, 2018 Category: Genetics & Stem Cells Authors: Todd Harris Tags: news micropublication Source Type: news
Data explained: gene descriptions
WormBase writes and displays short summaries about genes, in the ‘Overview’ widget on the very top of gene pages. When we realized we couldn’t keep up with both updating and writing new gene descriptions, we developed an automated gene descriptions data pipeline that looks at primary data from the most recent WormBase release, in order to write gene descriptions for the next WormBase release (eg., the gene descriptions for the WS262 release of WormBase are based on the WS261 WormBase data release). The data we currently include in a gene description are – orthology to human for C. elegans genes an...
Source: WormBase - January 17, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news data files data type WS262 Source Type: news
Specify genome locations with 30 nucleotides of flanking sequence!
Many of us have had the experience of trying to reconstruct what someone has done and been frustrated trying to find the exact sequence. Relative coordinates do not last: gene models often change so that “Leu234” in a protein is no longer there and our knowledge of genome sequence changes (or we are working with a different strains) so the EcoR1 site 5’ to your favorite gene is not there. There is an easy solution: always specify a location by sequence. Thirty nucleotides is sufficient in essentially all cases to uniquely locate the site. Your simple effort in specifying a genome location by sequence, when you are ...
Source: WormBase - January 11, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Source Type: news
Call to authors: provide complete information about genetic entities and reagents
WormBase requests that authors provide complete information about genetic entities such as strains, alleles, transgenes, etc., in published papers. Providing a clear list of the experimental genetic entities used, in the paper, along with complete information about them would make curating your paper easier and quicker, saving time and effort that curators spend in searching for such information and/or writing to authors. For example, if you use strains, please provide the complete list of strain names and their genotypes, including transgenes, markers and any additional components. Papers with incomplete information about...
Source: WormBase - January 9, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Uncategorized Source Type: news
Latest chapter in WormBook about cell movement
Check out the latest chapter of WormBook in Genetics-‘Invading, Leading and Navigating Cells in Caenorhabditis elegans: Insights into Cell Movement in Vivo‘, by David R. Sherwood and Julie Plastino. (Source: WormBase)
Source: WormBase - January 5, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest wormbook Source Type: news
Where to look: C. elegans interaction data
If you are looking for interaction data for C. elegans look no further than our FTP site. At every release WormBase deposits data files on the FTP site under the relevant release number and species directories. The files are named after the data they contain. The interactions file for C. elegans for the WS261 release can be found here and is called c_elegans.PRJNA13758.WS261.interactions.txt.gz (Source: WormBase)
Source: WormBase - November 29, 2017 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news data files interactions WS261 Source Type: news
Latest chapter of WormBook on the cell biology of the mitochondrion now available
The latest chapter of WormBook is now available: Cell Biology of the Mitochondrion by Alexander M. van der Bliek, Margaret M. Sedensky and Phil G. Morgan. (Source: WormBase)
Source: WormBase - November 3, 2017 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest wormbook Source Type: news
WormBase Release WS261
We would like to announce the availability of the WormBase WS261 release on the WormBase website and FTP.
Some of the highlights of this release are:
C.briggsae curation
Manual curation of C. briggsae has continued, concentrating on genes with low levels of curation.
curation example for dicistronic loci
The WormBook chapter “Operon and non-operon gene clusters in the C. elegans genome” describes SL1-type operons and dicistronic mRNA loci. These look like a single gene containing two isoforms with little or no overlap. During the examination of the C. briggsae gene structures about 30 novel, conserved examples of thes...
Source: WormBase - November 2, 2017 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: new datasets new features news release notes new release WS261 Source Type: news
Alliance of Genome Resources Opens Door with Version 1.0 Release
The Alliance of Genome Resources (the Alliance) announces the release of the Alliance of Genome Resources website 1.0 – providing unified access to comparative genetics and genomics data from the Alliance data resources (www.alliancegenome.org). The Alliance brings together the efforts of the major National Institutes of Health NHGRI-funded Model Organism Database (MOD) groups, and the Gene Ontology Consortium, in a synergistic integration of expertly-curated information about the functioning of cellular systems. Our focus is to facilitate the use of these data towards better understanding of human biology and diseas...
Source: WormBase - October 26, 2017 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: community news Alliance of Genome Resources Source Type: news
Save the date: Annual French C. elegans Meeting
The 21st edition of Ver Midi will be held at the CIML, Marseille on Friday 26th January 2018, with Henrik Bringmann as invited speaker. It will be preceded by a workshop on high-throughput methods on the 25th, sponsored by Union Biometrica and TECAN.
The website for registration will open in November.
Please contact the organisers, Nathalie Pujol, Jonathan Ewbank or Vincent Bertrand if you wish to be added to the Ver Midi mailing list. (Source: WormBase)
Source: WormBase - October 12, 2017 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: community meetings news workshop Source Type: news
