New data: male neural connections in WormBase

The WS220 release of WormBase contains release 2 of the Male Wiring Project (MWP), at the Albert Einstein College of Medicine. This data consists of neural connections found in the adult male tail. It adds 8,400 pair-wise connections to WormBase , taking the total to 22,500 connections. All neural connection data in WormBase can be accessed using NeuroBrowse, an interactive graphical tool. A link to NeuroBrowse is on the relevant anatomy pages or it can also be directly launched. A brief user guide for NeuroBrowse is on our wiki. We thank MWP for sharing data with WormBase. Please visit the MWP web site for updates and additional information.

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.