We’ve added a Genome Browser instance for the draft genome sequence of Trichinella spiralis. T. spiralis is an obligate parasite of rats, pigs, bears, and humans that causes the disease trichinosis.
New release of WormBase: WS226
WormBase has been updated to the WS226 release of the database. Please see the release notes on the WormBase Wiki.
Private instances of WormBase in 10 minutes
Are you interested in running your own private instance of WormBase without having to work through a lengthy and complicated installation procedure? The Amazon Elastic Compute (EC2) Machine Images (AMIs) of WormBase are your answer.
Please see this Worm Breeder’s Gazette post for an overview of the process and this blog post for a detailed walkthrough.
Questions? Please drop me a line by email (todd@wormbase.org) or Twitter (@tharris).
Announcement: C. elegans Neurobiology Meeting
Details for the 2012 C. elegans Neurobiology meeting are below:
When: 14-17 June 2012
Where: EMBL Advanced Training Centre, Heidelberg, Germany.
Speakers:
Joy Alcedo
Leon Avery
Alexander Gottschalk
Lindy Holden-Dye
Josh Kaplan
Ikue Mori
Stephen Nurrish
Piali Sengupta
Kang Shen
Organisers:
Jean-Louis Bessereau
Gert Jansen
William Schafer
The website and a poster will soon be released.
SPELL – A display and clustering tool for large scale gene expression data.
SPELL (Serial Pattern of Expression Levels Locator) is a display and clustering tool for large scale gene expression data, including microarray, tiling array and RNAseq. The software is developed and maintained by Matt Hibbs from the Jackson Laboratory. SPELL can now search for worm microarray and RNAseq data.
The current functionalities of SPELL include:
1. Checking expression levels of individual genes in each dataset
2. Searching for other genes with similar expression profiles
3. Identifying biological processes related to the query genes
4. Users can download individual datasets
SPELL users can enter a list of genes that are expected to have similar expression profiles. SPELL checks the correlation of these genes in each dataset. The dataset with the highest correlation will get the most weight. If users provide only one gene, all datasets will get the same weight. Based on the weight of each dataset, SPELL will identify other genes with similar expression profiles, and display biological process gene ontology terms that are enriched in the results. SPELL provides gene-centric microarray and RNAseq data that are mapped to the current WormBase release. WormSPELL226, released on July 29th, contains 3 RNAseq datasets and 112 microarray datasets, including 1726 microarray experiments and 58 RNAseq analyses.