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 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

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 our new tissue enrichment analysis tool!

We are pleased to announce our new web-based tool ‘TEA‘, this tool has been developed for identifying enrichment of C. elegans tissues among gene sets.  The software is also available for download.  Description of the tool is published here.

Introducing a new genome browser for WormBase

JBrowse

We are pleased to introduce a new genome browser that we are currently testing as a replacement for the current, long serving genome browser (GBrowse). The new browser, an implementation of JBrowse from the GMOD project, is currently available at wormbase.org/tools/genome/jbrowse/.  The new genome browser has a fast and pliable user interface; becoming oriented to the new browser should be relatively painless as it shares many design features in common with the current browser.

The new genome browser also has new functionality not available in the old one.  Key among these are (all of which are available from the genome browser’s file menu):

  1. Opening many types of data files (GFF, BAM, BigWig/BigBed, VCF), without having to upload them (so it’s *fast*).
  2. Creating combination tracks, where the contents of any two tracks can be combined using set or arithmetic operations.
  3. Making a sequence (DNA or amino acid) search track that will highlight when a motif is present (the search string can take the form of regular expressions–please let us know if you’d like help writing a regular expression).

Other useful features include the ability to “pin” a track to the top of the browser so it won’t scroll off the top of the page (simplifying visual comparisons with other open tracks), and a “full page” button that will open a new browser window where the genome browser takes up the full page.

Please try out the new browser and give us any feedback you can think of, either things you’d like to see, things you don’t like, whatever.