We are excited to announce that the beta version of the new WormBase site that was opened for testing six months ago will go live on March 30th. We understand that it may take some time to adjust to the new interface, but hope that the improved organization, customizability, and speed of the site will ease the transition. Once the new website is released, the current (old) website will be frozen at version WS230 and made available for the foreseeable future. We will continue to refine and expand the new site with exciting new features throughout 2012. As always, we welcome all comments and suggestions at [email protected].
You can find data files on our FTP site
We would like to remind users that our FTP site provides access to various data files. WormBase has recently improved the organization of it’s FTP site so that users can easily browse and find different data files. We have made nearly every file directly accessible without needing to know what the current version of WormBase is. For example, the following link will always point to the most current release of WormBase:
ftp://ftp.wormbase.org/pub/wormbase/releases/current-www.wormbase.org-release.
You can also access files related to different genomes for a given release, for example you can go to the C. elegans or C. briggsae specific directories.
WormBase seeks a Biological Curator
WormBase at Caltech (at Pasadena, CA, USA) currently has seven full-time biological curators as well as several bioinformaticians and software developers. The Caltech group annotates gene expression patterns, gene regulation, functional descriptions, phenotypes, microarray data, cell functions, and protein and gene interactions. We continually try to obtain, store and display whatever information has become most relevant to our community.
We are seeking an individual with substantial C. elegans experience to help analyze gene functions and interactions and incorporate them into WormBase. Curation places a premium on broad scientific knowledge, excellent communication skills, and creative intelligence, as well as on patience and hard work. Computer literacy in UNIX or Linux and in Perl is a plus, but is not required, since curators have the opportunity to develop their skills in bioinformatics at Caltech. While demanding high skill and willingness to serve others, biological curation at Caltech also offers rewards beyond that of a postdoc, one of which is a wide range of future job prospects: biologists who become curators can remain at the forefront of research, and also have the option to move to bioinformatics. A curator’s salary is higher than most postdoc’s, and the general quality of life in Pasadena and Caltech is good. Curators at Caltech work in an excellent academic environment, where they can interact with several laboratories carrying out genomics both at Caltech itself and at affiliated institutions.
Please contact Paul Sternberg ([email protected]) for more information.
Share your knowlege about worm web resources
WormBase is collecting information about web resources for worm researchers. If you either run, or know of  an internet-accessible resource that provides information or performs functions useful to the research of C. elegans or other nematodes, please submit this information to [email protected]. We plan to construct ‘yellow pages’ for these web resources, so help us with this effort!
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.