New SPELL server: Fresh look and faster

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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 has collected over 6,000 experiments for 9 nematode species. Users can also download these datasets for their own analysis. See WormBase SPELL Tutorial: http://wiki.wormbase.org/index.php/SPELL
The new WormBase SPELL server is twice as fast as the old version. Please give it a try and let us know what you think!

 

High throughput datasets in SPELL now searchable based on topic

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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).

Check out the Eukaryotic Genomic Databases book!

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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.

Registering Lab, Strain and Allele designations

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If you would like to register a new lab and/or receive strain and allele designations please consult the WormBase documentation page here.  This page also describes the nomenclature that WormBase requires and uses to describe genes, alleles, strains, gene knockouts, modifiers (suppressors, revertants and enhancers), and chromosomal aberrations (duplications, deficiencies, inversions and translocations) .