Help us by acknowledging WormBase in your publications.

We would like to enlist your help in ensuring that WormBase continues to exist and is successful. You can do this by explicitly acknowledging WormBase in each of your papers when you have used it in the planning, design, execution, analysis, or reporting of the research described.

This simple task will help us make the case to administrators at NIH and others for the utility of WormBase. You can do this in two ways:

1. Include in your acknowledgments, a statement thanking WormBase, ‘We thank WormBase’. To save characters, it can be included in a list:  ‘We thank XYZ for reagents, ABC for comments and WormBase’. If this is a problem, just mention the particular WormBase release (WSnnn) in the text.  When you use these methods, the acknowledgements of WormBase are amenable to searching and reporting.

2. As a reviewer or editor, you could check that WormBase is acknowledged, if appropriate.

Thanks for your help!

Another record year for WormBase: over 50 million pages served.

Curious about how many people use WormBase and how often? Me too.

I just finished compiling the access statistics for 2010. Last year, WormBase served 51,606,849 distinct pages. This is a dramatic increase over 2009 (34,106,168) pages and continues the trend seen over the last few years. Note: spiders, web-crawling robots, and programmatic data-mining requests are excluded from these tallies.

We have some great things planned for our user community this year, including a ground up re-design of the site designed in part to meet this growing demand.

WormMart is under redevelopment

We know that several of our users have had problems using WormMart.  We would like to alert users to the fact that WormMart is under redevelopment, some data-sets are  unavailable and there are bugs in the tool that we know of and are actively working on.  Developers aim to build a new release before the end of the year.  We are sorry for this inconvenience.

Did you know that WormBase provides useful data files for download?

WormBase maintains a public FTP site where you can find many commonly requested files and datasets, the WormBase software and prepackaged databases. DNA sequence data for the genomes of C. elegans, C. briggsae, C. remanei, etc., are available in FASTA format, as is protein data.  Microarray data like the up-to-date mapping of microarray probes to WormBase genes for Affymetrix, Agilent, Washington University Genome Sequencing Center and Stanford Microarray Database (SMD) chips, is also made available.  For C. elegans, the following files are down-loadable from the FTP site: confirmed_genes — which lists curated C. elegans genes that have been confirmed by transcriptional data; wormpep — FASTA-format files containing predicted and confirmed protein translations, and many other files.

Take a look at our FTP site at ftp://ftp.wormbase.org/pub/wormbase/.  Be sure to look at the README file in each directory for a listing of the contents of that directory.

Genomes in WormBase

In addition to C. elegans, WormBase provides several resources for viewing and obtaining genome information for different worm species. WormBase classifies genomes in various tiers depending on the amount of curation effort it is able to spend on maintaining them.  For a description of the various genomes either in, or coming to WormBase, their current status and the resources available for each, please visit http://wiki.wormbase.org/index.php/WormBase_Genomes.