New and Improved Author First Pass Pipeline!
Community curation is a valuable part of WormBase. For the past ten years, C. elegans researchers have participated in our ‘Author First Pass’ pipeline using a web-based form to alert WormBase curators to entities and data types in their newly published papers. We are very excited to announce a new and improved ‘Author First Pass’ pipeline that uses the Textpresso Central text mining system to automatically extract entities and identify data types in new C. elegans papers. As before, corresponding authors will receive an email (Help WormBase curate your paper!) shortly after publication of thei...
Source: WormBase - June 5, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community new features news author first pass data type text mining Textpresso Source Type: news

Come and talk to WormBase staff at the IWM 2019!
It’s that year again when worm breeders and worm lovers will be at UCLA from June 20th-24th for the International Worm Meeting. WormBase will be there in full force and will participate in several events–talks, workshops and booths. WormBase staff will be at our booth during the poster sessions in Pauley Pavilion, come talk to us and feel free to ask any questions related to data and data querying and give us your suggestions and comments. Also, take the opportunity to visit the microPublication booth and find out how to micropublish your results. WormBase related events at IWM 2019 include– Thursda...
Source: WormBase - June 3, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community meetings news Source Type: news

New VC2010 and improved CB4856 genomes published
The VC2010 genome assembly has just been published in Genome Research as an open-access article. This assembly is largely derived from a completely isogenic VC2010-derived strain, PD1074, that is now available from the CGC. In related news, Junho Lee and his lab have simultaneously published an open-access article on their substantially improved genome assembly for Hawaiian C. elegans (CB4856). (Source: WormBase)
Source: WormBase - May 24, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news paper of interest genomes new genome Source Type: news

UC Davis features micropublications
microPublication.org publishes brief, novel findings, negative and/or reproduced results, and results which may lack a broader scientific narrative. Each article is peer reviewed and assigned a DOI. Included data is curated and, upon publication, deposited in third party referential databases (when available). Recently UC Davis featured an article, ‘Small Science Snippets: Micropubs Help Share Discoveries‘ about how one of their researchers used a micropublication to publish their results. Micropublish your results today! (Source: WormBase)
Source: WormBase - May 17, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news micropublication Source Type: news

WormBase updated to the WS270 release
Alliance orthologs Starting from WS270 we are using the Alliance of Genome Resources for orthologs between model organism genes. This should be more comprehensive and include the latest data from our sister databases. VC2010 genome An assembly and geneset of the VC2010 C.elegans strain has been added and work is ongoing to improve the integration and display of strain specific data. Additionally more mappings of N2 annotation will be included in future releases. (Source: WormBase)
Source: WormBase - May 15, 2019 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: news release notes Alliance of Genome Resources WS270 Source Type: news

An appreciation of Sydney Brenner
See this beautiful appreciation of Sydney Brenner by Peter Lawrence in DEVELOPMENT.   (Source: WormBase)
Source: WormBase - May 10, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news research community Sydney Brenner Source Type: news

SGD turns 25!
25 years ago the SGD (The Saccharomyces Genome Database) went online.  Happy Birthday SGD! SGD provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms. SGD collaborates with WormBase on several database-related projects including the Alliance of Genome Resources.  Check it out! (Source: WormBase)
Source: WormBase - May 8, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news Alliance of Genome Resources SGD Source Type: news

Short WormBase downtime yesterday
WormBase went down at 2.54pm ET yesterday. The problem was caused ironically by a fault recovery mechanism that was introduced recently. The fault recovery mechanism takes faulty servers out of service and replaces them with healthy ones. The process involves two components:the detection of faulty servers and the creation of new ones. Two simultaneous problems in the two components lead to the failure. A false positive in detecting the faulty server caused the sever to be taken out of service, and a missing hard drive snapshot caused the failure to start new servers. To avoid such future occurrences we are looking into way...
Source: WormBase - May 8, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Source Type: news

New chapter in WormBook, GENETICS, on sensing of physical stimuli in C. elegans
Check out the new chapter in WormBook, GENETICS–‘How Caenorhabditis elegans Senses Mechanical Stress, Temperature, and Other Physical Stimuli‘ by Miriam Goodman and Piali Sengupta. (Source: WormBase)
Source: WormBase - May 7, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest wormbook Source Type: news

Tuesday, April 30th – early registration deadline for IWM 2019
Please note that Tuesday, April 30th is the deadline for early registration for the International C. elegans conference at UCLA. (Source: WormBase)
Source: WormBase - April 29, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community meetings news IWM Source Type: news

Sydney Brenner passes away
Sydney Brenner, the Nobel prize-winning molecular biologist who pioneered the use of C. elegans as a model organism has passed away. https://www.nature.com/articles/d41586-019-01128-3 (Source: WormBase)
Source: WormBase - April 8, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news Source Type: news

WormBase is up to date with curation of protein-protein interactions
We have now curated all C. elegans protein-protein interactions (physical) from the published literature. In the current release, WS269, we have over 30,000 binary gene pair interactions. Please let us know if we have missed anything! (Source: WormBase)
Source: WormBase - March 29, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news curation protein interaction Source Type: news

Important Dates for the 22nd International C. elegans Conference
The abstract submission deadline for the 22nd International C. elegans Conference is March 28th! The conference will be held June 20-24, 2019 at UCLA. For more information visit the conference website. Abstract Submission Deadline: March 28 Submit an abstract Registration Discounted early registration: April 30 Discounted advance registration: May 1 – June 17 Register for the conference Housing Reservations Deadline: May 15 Make a housing reservation (Source: WormBase)
Source: WormBase - March 23, 2019 Category: Genetics & Stem Cells Authors: Todd Harris Tags: meetings news Source Type: news

Getting DNA sequence from JBrowse
There are two ways that users can download DNA sequence from JBrowse: in relation to a feature, like a gene, or by specific sequence coordinates. Getting Sequence for a Gene or Transcript To get the sequence for a gene, open any of the “Curated Genes” tracks and right click or control click on the feature and select “View Sequence” from the resulting popup menu. If you are using the main “Curated Genes” track, you’ll get a dialog box asking which transcript you want to view. It does this because it needs to know what subfeatures like exons and introns can be shown. If you’re ...
Source: WormBase - March 19, 2019 Category: Genetics & Stem Cells Authors: Scott Cain Tags: brief communication news tutorials jbrowse Source Type: news

New GENETICS WormBook Chapter on Developmental Control of the Cell Cycle
Check out the new chapter of WormBook in GENETICS– ‘Developmental Control of the Cell Cycle: Insights from Caenorhabditis elegans‘ by Edward T. Kipreos and Sander van den Heuvel. (Source: WormBase)
Source: WormBase - March 11, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news wormbook Source Type: news

Gene Ontology Consortium turns 20
The Gene Ontology (GO) resource turns 20! Check out the latest paper describing this resource.  WormBase uses GO to describe the molecular function, cellular localization and the biological processes that a gene is involved in.  These annotations are displayed in the Gene Ontology widget on all gene pages in WormBase.  The ontology structure including the number of genes annotated to each term can be viewed via tools such as the Ontology Browser. GO Enrichment Analysis can be performed using tools on the GO website.  Data files (known as gene association files) of all the GO annotations in the latest Wo...
Source: WormBase - March 8, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news gene ontology Source Type: news

Paper of Interest: Identification of functional long non-coding RNAs in C. elegans.
This paper predicts 143 new multi-exonic lncRNA loci in C. elegans, along with ~3,000 possible new single-exon lncRNA loci.   (Source: WormBase)
Source: WormBase - March 1, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest Source Type: news

Biocurator position open at WormBase
A biocurator position is open at WormBase.  If you are interested and for further details please contact Paul Sternberg at pws@caltech.edu (Source: WormBase)
Source: WormBase - February 8, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news positions available Source Type: news

Integrated model organism data at the Alliance of Genome Resources
It is now possible to view integrated data from six different Model Organism Databases (MODs) and the Gene Ontology (GO) Consortium at the Alliance of Genome Resources (Alliance).  One can view gene descriptions, disease model data, orthology data, gene expression data and much more for the six major model organisms (yeast, worm, fly, zebrafish, mouse, rat) as well as human data on gene pages at the Alliance.   You can search by gene, disease or a GO term and be taken to a page where you will find integrated views of data relevant to all of the above mentioned organisms.   For example, searchi...
Source: WormBase - February 7, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news Alliance of Genome Resources Source Type: news

New gene descriptions for the WS268 release of WormBase
The WS268 release of WormBase features new automated gene descriptions (displayed in the ‘Overview’ widget at the top of the gene page). In addition to the code being entirely rewritten, we have also added gene descriptions for a new worm species – Trichuris muris.   These automated gene descriptions are highly structured and are based on curated data such as orthology data, Gene Ontology (GO) annotations, Disease Ontology (DO) annotations, gene expression data, etc., in WormBase. The following data-types are included in the description of a given gene, when available: orthology to human ge...
Source: WormBase - January 14, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new datasets news WS268 Source Type: news

WormBase updated to the WS268 release
Please note that the WormBase website has been updated to the WS268 release.  Details about this release may be found in the Release Notes for WS268.  The notes include a list of files that we publish on our FTP site. (Source: WormBase)
Source: WormBase - January 13, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news release notes new release WS268 Source Type: news

New chapter of WormBook in GENETICS
Check out the new chapter of WormBook in GENETICS about mitotic cell division by Lionel Pintard and Bruce Bowerman – ‘Mitotic Cell Division in Caenorhabditis elegans‘. (Source: WormBase)
Source: WormBase - January 11, 2019 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news wormbook Source Type: news

Paper of Interest: Comparative study of 81 genomes of parasitic and non-parasitic worms
Check out the paper ‘Comparative genomics of the major parasitic worms’ in Nature Genetics by the International Helminth Genomes Consortium and the ‘News and Views’ article by Paul Sternberg, ‘Opening up a large can of worms‘. (Source: WormBase)
Source: WormBase - December 5, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest genomes parasite genomes Source Type: news

Update on protein-protein interaction data in WormBase
Currently WormBase contains over 28,000 physical protein-protein interactions of which 1,500 protein-protein interactions have been curated by BioGRID as a collaboration with WormBase. Within the data set, over 17,000 protein-protein interactions are unique, and over 6,000 unique genes are involved in these interactions. In WormBase, protein-protein interaction data can be found as a subclass of physical interaction data in the ‘Interactions widget’ on the gene report page. The interactions widget provides all types of interaction data related to the gene of interest, such as physical, genetic, regula...
Source: WormBase - November 28, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest tutorials protein interaction WS267 Source Type: news

New SPELL server: Fresh look and faster
Please note that we have moved the WormBase SPELL tool to a new server on the Amazon Cloud: https://spell.wormbase.org.  This should not affect any of our users, as the ‘Tools’ link on the main WormBase menu bar will take you to this new URL. SPELL (Serial Pattern of Expression Levels Locator) is a query-driven search engine for microarray, RNAseq and Proteomics data. Given a small set of query genes, SPELL identifies which datasets are most informative for these genes, then within those datasets, additional genes are identified with expression profiles most similar to the query set. WormBase SPELL h...
Source: WormBase - November 16, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news tutorials SPELL tools Source Type: news

WS267 release of WormBase
Please note that the WS267 release of WormBase is now live. Trichuris muris update Trinity assembled RNASeq reads from publicly available short read data at SRA have been added to Trichuris muris as additional track and alignments. In addition IsoSeq data from long-range PacBio data (provided by the Berriman lab), corrected by genome alignment has been used as additional source to build transcript models. In addition the Trichuris muris ncRNA gene set has increased from 26 to 759 following the integration of data produced by the WormBase Parasite ncRNA prediction pipeline. These transcripts have been fully integrated with ...
Source: WormBase - November 12, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: news release notes WS267 Source Type: news

WormBook in GENETICS
From Iva Greenwald: Three years ago, I announced in this column the creation of WormBook in GENETICS, thanks to a generous funding commitment to our community by the Genetics Society of America. Please look at what we’ve done so far and you’ll see what a great resource it is:  http://www.genetics.org/content/wormbook We are really hitting our stride now, and you will see WormBase announcements of new chapters increasing apace.  The more you demonstrate the value of WormBook through viewing, downloading, and especially, citing the articles, the more the GSA will understand the value of their sponsorshi...
Source: WormBase - October 17, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news wormbook Source Type: news

New chapter of WormBook in GENETICS
Check out the new chapter of WormBook in GENETICS: From “the Worm” to “the Worms” and Back Again: The Evolutionary Developmental Biology of Nematodes by Eric Haag, David Fitch and Marie Delattre. (Source: WormBase)
Source: WormBase - October 5, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news wormbook Source Type: news

WS266 release
Please note that the WS266 version of WormBase has been released. Go to the release notes for this release to view a list of data types and their numbers. A list of all files available on our FTP site can also be viewed.  Changes in this release include the following: Physical Interaction data curation We have added over 5000 manually curated physical interactions which include binary protein-protein interactions as well as protein interactions that occur in a protein complex. Protein-protein interaction data can be found as a part of physical interaction data in the Interactions widget on the gene page. The Interacti...
Source: WormBase - September 18, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: news release notes WS266 Source Type: news

Paper of Interest: OrthoList 2
The new comparative genomic analysis between C. elegans and humans, OrthoList 2 (OL2), was just published early online in GENETICS.  OL2 comes with a new web-based tool that allows for rapid searches of OL2 by worm or human gene identifiers, protein domains (InterPro and SMART), or human-disease associations (OMIM), and also includes updated RNAi resources. The paper describes OL2 and various findings, including how the content of OL2 compares with the original OrthoList tool. The web-based tool for accessing OL2 is here. (Source: WormBase)
Source: WormBase - August 22, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: news paper of interest orthologs Source Type: news

WS265 release
loci with two different protein products There are a small number of loci which code for two very different protein products. These include dicistronic mRNA operons and loci which have a few small exons in common then have alternate splicing leading to many different exons being used. The details of some of these can be found in the WormBook chapter “Operon and non-operon gene clusters in the C. elegans genome”. Previously, these have been curated as isoforms of a single gene. This was causing problems because the description of gene function would be based on one isoform, leaving the other isoform undescr...
Source: WormBase - July 20, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: news release notes WS265 Source Type: news

Check out the latest chapter on microRNAs in WormBook
Check out the latest chapter in WormBook, GENETICS: Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs by Victor Ambros and Gary Ruvkun. (Source: WormBase)
Source: WormBase - July 5, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest wormbook Source Type: news

High throughput datasets in SPELL now searchable based on topic
Data sets coming from high throughput experiments which reside in SPELL have now been updated with topics so that you can actually search by your favorite topic.  You can see the topic search options by clicking the button ‘Options for Filtering Results by Dataset Tags‘ on the SPELL home page under the search box  for Gene Name(s). (Source: WormBase)
Source: WormBase - May 22, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news tutorials high throughput dt SPELL Source Type: news

Which WB tool to use -check out our updated list and links
If you’re wondering which WormBase tool to use for your data needs, check out this updated list of tools with short descriptions for what to use them for.  Click on the tool names to be taken directly to the tool. (Source: WormBase)
Source: WormBase - May 18, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news tutorials tools Source Type: news

Guest Blog: New Nematodes in WormBase
  This WS264 release of WormBase includes two new genome assemblies from both a free-living Caenorhabditis species (C. nigoni) and a whipworm parasite of mice (Trichuris muris). The C. nigoni genome was assembled from both long-read (Pacific Biosciences) and short-read (Illumina) data, and then further scaffolded by genome-wide alignment with its very close relative, C. briggsae. Despite the fact that C. nigoni and C. briggsae are closely enough related to produce partially fertile offspring, their lifestyles and genomes are quite different.  C. briggsae, like C. elegans, is primarily a self-fertilizing hermaphro...
Source: WormBase - May 16, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: news guest WS264 Source Type: news

Check out the Eukaryotic Genomic Databases book!
The Eukaryotic Genomic Databases book has just been released by Springer (Editors: Kollmar, Martin) and contains detailed chapters related to the eukaryotic databases such as WormBase, FlyBase, the yeast databases, SGD and PomBase, etc. The chapters describe database contents and classic use-cases, which assist in accessing eukaryotic genomic data and encouraging comparative genomic research. (Source: WormBase)
Source: WormBase - May 15, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest tutorials book genomes Source Type: news

WS264 release
C. elegans sORFs sORFs.org is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). It contains predicted sORF regions for several species, including C. elegans. We have annotated 118 predicted sORF regions as coding (CDS) isoforms of the existing genes. It is likely that in the next release, where these isoforms do not overlap with existing isoforms, these sORF regions will be changed to be individual genes and not isoforms. 52 of these annotated sORF regions do not start with the canonical Methionine AUG initiation codon. It is possible that they use a non-canonical initiat...
Source: WormBase - May 14, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: new datasets news release notes new release WS264 Source Type: news

Include strain names in publications!
We urge you to explicitly state strains used in your experiments to foster reproducibility and to help WormBase biocurators get your results into WormBase.  Historically, C. elegans researchers just stated the alleles used, based on the reasonable idea that all strains were close to Brenner’s N2.  As the years and hundreds of worm generations passed, strains diverged.  We usually don’t know the full genotype of our strains (and really won’t even with whole genome sequencing since copy number variation is often hard to detect). Including strain names will greatly help sort out any background...
Source: WormBase - April 26, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news data request strain Source Type: news

Wondering how to cite WormBase?
If you are looking to cite WormBase please take a look at: https://wormbase.org/about/citing_wormbase#012–10. This can also be accessed from the Menu at the bottom of the WormBase home page on the extreme left, under WormBase–>How to cite.  Please do explicitly acknowledge WormBase in your published work when you have used it in the planning, design, execution, analysis, or reporting of the research described.  We can then search for these acknowledgements and use these numbers in various reports, eg. for funding agencies, etc. (Source: WormBase)
Source: WormBase - April 25, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Source Type: news

Please specify allele and strain names in publications
WormBase curates data from published papers and attaches different types of data such as phenotype, overview, expression, human disease model, etc., to genetic entities such as genes, alleles, strains or transgenes. These are also bonafide  ‘objects’ in our database which allow us to attach data to them.  If we cannot find these named genetic entities in your paper it becomes extremely difficult for us to curate the paper.  It is not enough to just specify the amino acid or nucleic acid change of a mutation, we need either the strain or allele name to curate the paper. (Source: WormBase)
Source: WormBase - April 10, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news data request paper Source Type: news

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 i...
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 PantherD...
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 gene...
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 sequenc...
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