The next webinar held by the Data Coordination Center for modENCODE is scheduled on Thursday Mar 1, 12:00 EST, Topic: “Understanding worm and fly transcriptome data.” This webinar will introduce participants to the transcriptome analysis data generated in Robert Waterston’s lab (C. elegans) and Susan Celniker’s lab (D. melanogaster). Space is limited so advance registration is necessary. Please email help@modencode.org to reserve your spot. More details and the schedule are available on the modENCODE wiki.

We just finished bundling the latest Amazon EC2 AMI of WormBase for WS229. This AMI includes an updated genome browser, several new species, and of course all the databases and software necessary to run your own instance of WormBase. Search for WormBase on EC2 or for the AMI ID: ami-e9994980.

WormBase has been updated to the WS229 release of the database.

The newly published Bursaphelenchus xylophilus (Kikuchi et.al) is as of WS229 available at WormBase including it’s gene set. The data are available as GFF3 and FASTA files for download, and has been added to GBrowse and BLAST.

Bursaphelenchus xylophilus is a pine parasite causing considerable economic damage and can give insights into evolution of plant parasites by comparing it, for example, to Meloidogyne.

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.

The next webinar held by the Data Coordination Center for modENCODE is scheduled for Thursday Feb 2, 12:00 EST. Topic: “Using modENCODE tools: GBrowse and modMINE”. This webinar will discuss the web tools for data retrieval and analysis – data mining interface (modMINE) and genome browser (GBrowse) — both accessible via mod.encode.org. Space is limited so advance registration is necessary. Please email help@modencode.org to reserve your spot. More details and the schedule are available on the modENCODE Wiki.

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 (pws@caltech.edu) for more information.

WormBase has been updated to the WS228 release of the database.

I would like to draw your attention to f Karin Kiontke et al.’s new paper in BMC Evolutionary Biology  on the phylogeny and molecular barcodes for Caenorhabditis. The authors describe quite a few new strains and species, which should be of interest to anyone interested in phylogeny of nematodes.

But they couldn’t find any sister species to C.elegans, so that challenge is still on.

The newly published Ascaris suum genome (Aaron Jex, et al, Nature 2011 Oct 2) is available at WormBase including it’s geneset. The data has been added to GBrowse/BLAT/BLAST and can be downloaded as FASTA/GFF3 files from the WormBase FTP server.

Ascaris suum is a model for other parasitic Ascaris, as well as causing itself economic damage to pig farming. In addition it is known to be resistant to a large number of antihelminth chemicals.