WormBase News Archive: 2004

December 24, 2004: WormBase features described in new publication
New features to WormBase are described in a new manuscript "WormBase: a comprehensive data resource for Caenorhabditis biology and genomics, Chen et al." appearing this month in the annual Nucleic Acids Research Database issue. Access to the full text is free.
December 24, 2004: New release of WormBase, WS136
WormBase has been updated to the WS136 release of the database. This is the final data release for 2004. This release includes a new Gene Class display. This display makes it easy to see, for example, all genes that fall into the lin class (as well as genes previously included in this class).
December 26, 2004: Textpresso server is back on-line
Service to the Textpresso server (which powers literature searches at WormBase) has been restored. We apologize for any inconvenience this outtage may have caused.
December 24, 2004: Textpresso server temporarily unavailable
Due to technical difficulties, literature searches via Textpresso are temporarily unavailable. We are working on the problem and hope to have it resolved shortly. Posted 12.21.2004.
December 5, 2004: Initial batch of BCGSC GFP expression patterns available
The first set of GFP constructs and expression patterns from the BC C. elegans Gene Expression Consortium is now available. This set spans over 300 images with more images to be added to WormBase over the coming months. The Consortium is supported by funding from Genome BC / Genome Canada. See the expression pattern of xnp-1 for an example.
December 5, 2004: New release of WormBase, WS135
WormBase has been updated to the WS135 release of the database. New features include manually curated binding sites (visible on the Genome Browser). In addition, WormBase has been updated to the most recent release of the Uniprot database.
November 12, 2004: New genome-wide RNAi data set based on an ORFeome library available
The results from the systematic RNAi screen reported in PMID: 15489339, Rual et al., "Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library" are now available. There are 10951 experiments, 1066 of which showed a mutant phenotype. See MV_SV mv_AAB02615 for an example.
November 12, 2004: Genetic spans now available on the Genome Browser
To aid in positional cloning, the calculated genetic span of loci with two-factor positions are now displayed on the Genome Browser under the track "Genetic Limits". See III:7,502,125 for an example. Please note that these positions should be treated with some skepticism since they rely on interpolating the genetic map onto the physical map. Please send us your comments on this experimental feature!
November 12, 2004: New Release Of WormBase, WS134
WormBase has been updated to the WS134 release of the database. This release contains new RNAi experiments from Rual et al. (2004). The Genome Browser has been enhanced to display alternative splices in UTRs within gene models, along with a new experimental track the displays genetic spans.
October 30, 2004: New Release Of WormBase, WS133
WormBase has been updated to the WS133 release of the database. This release contains the first recalculation of reciprocal best blast match ortholog pairs between C. elegans and C. briggsae since the initial analysis. For an example, see the Gene Page entry for lin-29.
October 16, 2004: Three Week Release Interval
For a trial period lasting until the end of 2004, WormBase will be switching to a three week interval between data releases.
October 12, 2004: New Release Of WormBase, WS132
WormBase has been updated to the WS132 release of the database.
October 7, 2004: Genes Now Searchable By Descriptive Terms
In addition to searching for genes by name, users may now search using descriptive terms such as inducible, functional descriptions such as cancer, or proper names from other model systems such as bicoid. This facility draws from the recently added homology group data as well as manually curated concise descriptions of gene function.
September 27, 2004: Scheduled Network Outtage
Due to scheduled network maintenance at Cold Spring Harbor, WormBase (and the related development and data freeze sites) will be unavailable between 10 PM on October 2nd until approximately 6 AM on October 3rd. We apologize for the disruption.
September 27, 2004: WS130 Data Freeeze now available
WS130 has become the fourth "frozen" data release. It will be permanently accesible at http://ws130.wormbase.org/.
September 26, 2004: New Release Of WormBase, WS131
WormBase has been updated to the WS131 release of the database. WS131 introduces refined handling of C. elegans literature across the site and the introduction of new unique paper identifiers.
September 4, 2004: New Release Of WormBase, WS130
WormBase has been updated to the WS130 release of the database. As the next "freeze" release of the data and software, WS130 will be permanently archived at ws130.wormbase.org in the coming weeks.
August 24, 2004: C. briggsae genetics initiative
A group of labs with an interest in C. briggsae genetics is seeking input on an initiative to expand the genetic mapping tools available in this species. This effort will culminate with a grant proposal for the October 1, 2004 NIH deadline. Researchers whose current or planned research would benefit from such tools are encouraged to contact Eric Haag (ehaag@umd.edu).
August 20, 2004: New Release Of WormBase, WS129
WormBase has been updated to the WS129 release of the database.
August 2, 2004: Oligo set microarray probes now available
Affymetrix GeneChip and Washington University GSC microarray probe set information is now available in WormBase. The data can be accessed from the Reagents section of the Gene Summary and on the Genome Browser.
August 2, 2004: New Release Of WormBase, WS128
WormBase has been updated to the WS128 release of the database.
July 30, 2004: New Microarray Data Display
A new Microarray Results page has been developed to display the expanding microarray data in WormBase. Microarray data can also be viewed in the context of the Gene Summary within the Function section.
July 27, 2004: A New Site Map Summarizes Available Features
A new Site Map outlines the various searches and displays. Brief descriptions describe usage and the types of information available from each page or search. A link to the Site Map is available from the far right side of the main navigation bar.
July 19, 2004: New Release Of WormBase, WS127
WormBase has been updated to the WS127 release of the database.
July 8, 2004: New Release Of WormBase, WS126
The current release of WormBase, WS126, is the first new release since WS123 in May. WS126 introduces several new features including a new Site Map, new displays for Life Stage and Gene Regulation, and unified handling of authors and researchers. In addition, WS126 incorporates significant behind-the-scenes data model changes that streamline the handling of genes.
May 25, 2004: Next Release Of WormBase Delayed
Due to substantial changes to the underlying data model and the need for extensive testing, the next live release of the database will be WS126, arriving the week of July 5th. WS124 and WS125 will be available on the development server for users interested in testing these releases.
May 19, 2004: New Microarrays Now Available
The Genome Sequencing Center at Washington University has funding from NHGRI and HHMI to produce and distribute microarrays for use by C. elegans investigators. The arrays contain 60 mers designed to represent 20,966 C. elegans genes from WormBase release WS93 and are available for $90 (US). Additional information, inlcuding order forms, is available online.
May 18, 2004: West Coast Worm Meeting Registration
Registration for the 2004 West Coast Worm Meeting, to be held at the University of California, Santa Barbara, Aug. 21-24, is now available. The deadlines are Friday, July 2, midnight PDT for submission of abstracts, and Thursday, July 15, midnight PDT for early registration.
May 12, 2004: East Asia Worm Meeting Registration
Registration for the East Asia C. elegans meeting is now available. The meeting will be held from June 28th-July 1st on Awaji Island in Japan. The registration deadline is May 21st.
May 1, 2004: Caenorhabditis Genome Sequencing Update
The whole genome shotgun sequencing phase of C. remanei has been completed and the ~1.43 million reads can be searched using BLAST. Fosmid end reads are in progress to be followed by 2 rounds of automated finishing, which should result in a high-quality draft assembly by the end of the summer. C. japonica and CB5161 are being backcrossed and checked for heterozygosity. They are scheduled for whole genome shotgun sequencing in August and December.
April 21, 2004: Midwest Meeting Registration is open
The meeting will take place at the University of Kansas June 11-13, with an early registration deadline of May 21st. Information, online registration and abstract submission are available.
April 5, 2004: East Coast Worm Meeting Registration
Online registration for the East Coast Worm Meeting is now available. The meeting will take place June 11th-13th at Yale University. The registration deadline is May 21st.
March 29, 2004: New anatomy ontology browser
A new anatomy ontology browser is now available for browsing and querying the anatomy ontology. For example, view the ontology for the M1 motor neuron.
March 18, 2004: WormBase database server for data mining is up and running
A more powerful aceserver has been set up and is open for remote access, via both command line and scripts. The port for the ACeDB database is 2005 (host is aceserver.cshl.org). The method for GFF databases remote access will be announced shortly.
March 17, 2004: More mirrors, more freezes
The second WormBase mirror site has been set up at Caltech. This site, together with the first WormBase mirror site in Greece, will promote the accessiblity of WormBase worldwide. WormBase freeze version WS120 site has been set up. It's the third genome freeze site.
March 12, 2004: Launch of CisOrtho: a program for finding transcription factor binding sites
A HMMER based software for identifying transcription factor binding sites in C. elegans and C. briggsae. Read user manual (PDF file) and run program.
March 11, 2004: European Worm Meeting 2004 open for registration
The meeting will be held in Interlaken, Switzerland, 22-25 May 2004.
March 8, 2004: Sockeye new release generates PCR primers in C. elegans
Visit BCGSC for details. Sockeye is a 3D genome browser.
February 26, 2004: Another prize for Lincoln Stein, Co-PI of WormBase
Lincoln Stein has been named 2004 Benjamin Franklin Award in Bioinformatics laureate. He has also recently been named "Most Innovative in Biotechnology" by Genome Technology magazine.
February 6, 2004: Publication-quality images from the Genome Browser
The Genome Browser now generates publication-quality images in the Scalable Vector Graphics (SVG) format. SVG images can be resized with no loss in quality and edited in vector-based graphics applications. Follow the Publication Quality Image link from the main Genome Browser page for additional information.
February 6, 2004: Antibodies now available on the Gene Page
445 published antibodies, representing the initial curation effort of these reagents, are now available in the Reagents section of the Gene Page.
January 26, 2004: Sockeye Genome Browser release 1.1
This release by the Genome Sciences Center, Vancouver has features of particular interests to those wishing to perform alignments between C. elegans and C. briggsae. For details, read HOWTO (a PDF file).
January 26, 2004: Availability of K+ channel cDNAs and deletion strains
Please visit the Salkoff Lab website for details.
January 20, 2004: Meeting announcement
The Midwest Worm Meeting 2004 has been scheduled. For details about this meeting and other forthcoming worm meetings, please check Resources.
January 17, 2004: SAGE data are coming to WormBase
The Genome BC/Genome Canada-funded C. elegans gene expression project has released a collection of more than 1.6 million sequenced tags from 15 Serial Analysis of Gene Expression (SAGE) libraries for developmental stages, tissues and cell types. The SAGE data are currently available at http://elegans.bcgsc.bc.ca. They will appear in WormBase in the near future. Additional SAGE data will be added on an on-going basis.
January 12, 2004: Literature searches now powered by Textpresso
WormBase literature searches are now powered by Textpresso, seamlessly enabling direct searches of full text and abstracts. More information on Textpresso is available at Textpresso's home at CalTech.
January 12, 2004: More worm genomes to be sequenced
The NHGRI has approved the Washington University GSC to sequence three additional Caenorhabditis species: C. remanei, C. japonica and CB5161.
January 12, 2004: WS116 development version now available
WS116 will be a development-only release of the database due to extensive data model changes and the need for full testing. We invite interested users to test WS116 at dev.wormbase.org. WS117 will be the next live release of the database.
January 7, 2004: Final printed version of The Worm Breeder's Gazette
Volume 17 #5 will be the final printed issue of The Worm Breeder's Gazette. First published in 1975 by Bob Edgar and subsequently by the CGC , the Worm Breeder's Gazette played a major role in the early spread of information in the C. elegans community. Older versions will continue to be available online at the C. elegans WWW Server. The 2003 Genetic Map, published as part of the Gazette, is now available online.
January 7, 2004: WormBase publication describes new features
New improvements to WormBase are described in WormBase: a multi-species resource for nematode biology and genomics, a recent publication from the WormBase Consortium published in the 2004 Database issue of Nucleic Acids Research.
January 29, 2004: Lincoln Stein named "Most Innovative in Bioinformatics"
Lincoln Stein, co-PI of WormBase, was named "Most Innovative in Bioinformatics" in Genome Technology. The journal's honors are based upon nominations from Genome Technology readers, which include more than 20,000 professionals. For more information, visit Genome Technology.