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
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 their paper with a link ...
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–
Thursday Ju...
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
