You can find data files on our FTP site

by rkishore on January 18, 2012 · 0 comments

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.

Tagged as: data files, genomes

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ModENCODE Data Access Webinar, Feb 2nd, 2012

by tharris on January 17, 2012 · 0 comments

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.

Tagged as: modENCODE, webinar

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WormBase seeks a Biological Curator

December 23, 2011

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 [...]

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New release of WormBase: WS228

December 11, 2011

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

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Publication Spotlight: A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruit

December 8, 2011

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 [...]

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Ascaris suum genome in WormBase

December 5, 2011

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 [...]

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2012 C. elegans Development, Cell Biology, and Gene Expression Meeting

November 30, 2011

The next C. elegans Development, Cell Biology, and Gene Expression Meeting will be held on the campus of the University of Wisconsin-Madison, June 7-10.  Keynote Speakers will include Julie Ahringer, David Greenstein, Ken Kemphues, Craig Mello, Karen Oegema, Shai Shaham and Anne Villeneuve.  Organizers:  E. Jane Hubbard, Jeremy Nance, Martha Soto. http://www.union.wisc.edu/celegans/index2012.html

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Partial service interruption, Saturday 3 Dec 2011

November 28, 2011

To accomodate a storage upgrade, select elements of the WormBase website will be unavailable on Saturday, 3 December 2011 from 8:00 AM to 11:00 AM (ET; UTC -5). During this time, the following services will be unavailable: the Genome Browser; BLAST, BLAT, ePCR searches; the WormBase wiki; the WormBase blog; and the Worm Community Forum. [...]

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modENCODE Data Access Webinar: Dec 1st 2011

November 17, 2011

The next webinar held by the Data Coordination Center for modENCODE is scheduled for Thursday Dec 1, 12:00 EST. Topic: “Understanding worm and fly chromatin modification data”. It will give an introduction to the data obtained in studies of histone modification marks and chromatin binding proteins. Space is limited so advance registration is necessary. Please [...]

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Share your knowlege about worm web resources

November 4, 2011

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 raymond@caltech.edu. We plan to construct ‘yellow pages’ for these web resources, so help us [...]

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