WS249: reorganization of parasitic non-core species

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Starting with the WS249 release of WormBase we will point users to the new WormBase ParaSite portal for parasitic nematodes that are not curated as part of the WormBase core species.

Species that can now be found at WormBase ParaSite are:
Ancylostoma ceylanicum (PRJNA231479|PRJNA72583)
Ascaris suum (PRJNA62057|PRJNA80881)
Bursaphelenchus xylophilus (PRJEA64437)
Dirofilaria immitis (PRJEB1797)
Haemonchus contortus (PRJEB506|PRJNA205202)
Loa loa (PRJNA60051 )
Meloidogyne hapla (PRJNA29083)
Meloidogyne incognita (PRJEA28837)
Necator americanus (PRJNA72135)
Trichinella spiralis (PRJNA12603)
Trichuris suis (PRJNA179528|PRJNA208415|PRJNA208416)

Introducing a new genome browser for WormBase

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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.

WormBase HUBs

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As shown during the WormBase Workshops of the International Worm Meeting 2015 at UCLA:

(Slides/Notes of the WormBase ParaSite / HUBs section)

To enable use of up to date data on external sites, WormBase is providing with each release (starting with WS248), selected annotations and comparative tracks as assembly hubs.

there are currently two types of hubs,

the UCSC version:

and a version compatible with Ensembl Genomes (future WormBase ParaSite , Ensembl and BioDalliance releases)

(production HUBs are in synch with the current live WormBase release)

Introductory chapter added to WormBook

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Dear WormBook reader,

We are very happy to announce that A Transparent Window into Biology: A Primer on Caenorhabditis elegans, by Ann Corsi, Bruce Wightman, and Marty Chalfie, has just been added to WormBook as a co-publication with GENETICS. This concise and comprehensive review, which serves as an introductory chapter to WormBook, discusses the basic biology, genetics, anatomy, genomics, ecology, and evolution of C. elegans. Key discoveries resulting from research using this organism are described, as is the strong collaborative nature of the worm community. We expect this introduction to provide an invaluable resource for students and others new to C. elegans research and literature.

We thank Tracey DePellegrin, Ruth Isaacson, and Elizabeth De Stasio of GENETICS for their dedication to this collaboration, as well as Editor-in-Chief Mark Johnston for his support of the project.

Please proceed to read this new chapter and others on nematode biology at http://www.wormbook.org/. If you have any comments or suggestions, please submit them via the Feedback page on wormbook.org.

Jane