WormBase News Archive: 2003

December 30, 2003: Worm Meetings Announcement
Worm meetings in 2004 and the International Meeting in 2005 are now scheduled. Check Resources in the Links section for details.
December 22, 2003: WS116 Slightly Delayed
The WS116 release will be delayed until the first week of January due to extensive data model changes and the need for full testing.
December 13, 2003: C. elegans Course Announcement
The Cold Spring Harbor C. elegans Molecular Genetics Course for 2004 will be held July 27-August 16. The deadline for applications is March 15, 2004. Information about the course can be obtained at the course website.
November 23, 2003: CisOrtho, a orthologue-based transcription factor finder, is up for testing at the Dev site
CisOrtho is a software pipeline for finding binding sites for transcription factors, based on a user-defined set of known binding sites. Please comment.
November 17, 2003: C. briggsae Sequence Paper in PLoS
The Genome Sequence of Caenorhabiditis briggsae: A Platform for Comparative Genomics, by Lincoln Stein et al., has been published in PLoS. Also see a Synopsis in the same issue, and related articles published in The Scientist (1, 2), Genome Biology (Gupta and Sternberg), and Nature.
November 9, 2003: Initial Mos insertions now available
849 Mos-derived transposon insertions generated in the laboratory of Laurent Segalat are now available on the Genome Browser and on individual Allele pages.
October 29, 2003: UCSC C. elegans family browser available The University of California at Santa Cruz announces a protein family browser capable of finding genes based on their genomic proximity, their protein similarity, or the similarity of their expression profiles.
October 28, 2003: Intellectual C. elegans Researcher Lineage now available A list of each person's training lineage can be seen from the Person pages, for example, the Brenner page. You can add your information here.
October 27, 2003: New genome-wide RNAi data set based on RNAi-hypersensitive rrf-3 strain available
The results from the systematic RNAi screen reported in Simmer et al., PLoS Biology: Vol. 1, No. 1, e12 DOI: 10.1371 are now available for browsing and bulk download.
October 17, 2003: 2005 International C. elegans Meeting
Fifteenth International C. elegans Meeting will be held at the University of California at Los Angeles, June 25 (Saturday) - June 29 (Wednesday), 2005. The Genetics Society of America will be sponsoring the Meeting. Comments or questions can be addressed to Anne Marie Mahoney.
October 13, 2003: WormBase Receive 5-year NHGRI Grant
The National Human Genome Research Institute at the US National Institutes of Health has awarded WormBase a five-year grant to continue our efforts to provide easily-accessible, comprehensive information about C. elegans. More information can be found in the CalTech press release.
October 7, 2003: Negative Proteome Database adds C. elegans Proteins
The Negative Proteome Database, which allows researchers interactively explore the differences between the protein content of different species, now carries C. elegans in addition to fruitfly, yeast, human, mouse, arabidopsis, dictyostelium and a variety of prokaryotes. The database is still in beta stage: please report bugs to the database maintainer.
October 1, 2003: WS110 is Released.
This reference release will be available for perpetuity at http://ws110.wormbase.org and for download at ftp://ftp.wormbase.org/pub/wormbase.ws110 The first WormBase freeze is WS100.
October 1, 2003: New Website for the Nematode Community: NemATOL
NemATOL is an public database dedicated to collecting, archiving and organizing video images and other morphological information, DNA sequences, alignments, and other reference materials for the study of the phylogeny and diversity, taxonomy, systematics, and ecology of nematodes.
August 15, 2003: Deadline for New C. elegans Genetic Map Data
Deadline for inclusion in the 2003 Genetic Map of Caenorhabditis elegans is 31 August 2003. A printed version of the Map will be distributed by CGC as Vol 17#5 of the Worm Breeders Gazette. New gene and mapping data can most conveniently be communicated to the CGC online via WormBase
August 5, 2003: A Database of Pristionchus pacificus Genomics
Link to a new database of Pristionchus pacificus genomics has been put into the Links section on the front page.
August 1, 2003: C. elegans Structural Genomics
Proteins from the Structural Genomics Project are to be made available to the C. elegans community. Please send your feedback to them.
August 1, 2003: A C. briggsae Genetics Website
Link to a C. briggsae genetics website maintained by Bhagwati Gupta has been put into the Links section on the front page.
July 21, 2003: C. briggsae BLAST available
BLAST servers for the C. briggsae genomic and protein data sets are now available on the blast search page. A BLAT server has not yet been set up.
July 16, 2003: WormBase is Seeking Programmers
WormBase/Cold Spring Harbor has openings for 1-2 scientific programmers. We are seeking individuals with significant experience in bioinformatics, Perl and Web development. Please contact lstein@cshl.org.
June 19, 2003: C. elegans Gift Shop Grand Opening
Announcing the opening of the C.elegans gift shop. A shop dedicated to our favorite nematode. If you have any images you want to see on shirts, mugs, etc. please contact Ahna Skop.
June 14, 2003: WormBase Freezes Available
In the interests of providing stable data sets for whole genome analysis, WormBase will now be freezing the genome and its annotations with every 10th release (roughly two freezes per year). The first freeze is WS100, located at ws100.wormbase.org.
May 12, 2003: Public Access ACeDB Server Back Online
For access via AcePerl, there is now a public acess WormBase server at host aceserver.cshl.org, port 2005. See Linking & Mining WormBase for more details.
May 6, 2003: Allele Information Unified
WormBase now has unified its display of SNPs, transposon insertions and other alleles, and updated the allele detail page to provide molecular information about the mutation.
May 5, 2003: OST Alignments are now Online
WormBase now displays the nucleotide alignments of ORFeome v1.1 reads ("OSTs") to the genome. This data provides EST-like information about transcript splicing patterns.
June 11, 2003: WormBase Presentations at the International C. elegans Meeting
WormBase will be covered by a series of talks, posters, tutorials and a workshop at the 14th International C. elegans Meeting. A preliminary schedule is provided.
June 7, 2003: Nobel Prize Celebration Meeting, Sepember 9-10, 2003
To celebrate the award of the 2002 Nobel Prize to S. Brenner, R. Horvitz and J. Sulston, for their discoveries made using the nematode C. elegans, a symposium will be held in Cambridge, England.
May 20, 2003: RNAi Clone Library Now Available
The whole genome RNAi clone library described in Kamath et al. (2003) is now available from "MRC Geneservice".
May 20, 2003: International C. elegans Art Show
Everyone is invited to display your worm artwork during the poster sessions at the 14th International C. elegans meeting. For more information, contact Ahna Skop.
May 13, 2003: Physical Map Display Improved
The display of the C. elegans physical (cosmid fingerprint) map is now easier to get to. You can access it from the "Physically Mapped Clones" link of the gene page, or directly by searching for a cosmid name and going to the clone page.
May 12, 2003: Public Access ACeDB Server Back Online
For access via AcePerl, there is now a public acess WormBase server at host aceserver.cshl.org, port 2005. See Linking & Mining WormBase for more details.
May 6, 2003: Allele Information Unified
WormBase now has unified its display of SNPs, transposon insertions and other alleles, and updated the allele detail page to provide molecular information about the mutation.
May 5, 2003: OST Alignments are now Online
WormBase now displays the nucleotide alignments of ORFeome v1.1 reads ("OSTs") to the genome. This data provides EST-like information about transcript splicing patterns.
May 3, 2003: Worms Survive Space Shuttle Crash
The Washington Post reports that the C. elegans worms sent into space on the space shuttle Columbia for a synthetic nutrient experiment survived the shuttle's fiery reentry, and were recovered, reproducing happily, in their sealed containment vessels.
April 26, 2003: New Strain and Rearrangement Pages
WormBase now features pages for viewing experimental details of genetic rearrangements and strains.
April 24, 2003: C. briggsae Pages Improved
The C. briggsae gene, sequence and protein pages are now similar to the corresponding C. elegans pages.
April 18, 2003: Elegans/Briggsae Synteny Viewer Available
A early version of a synteny viewer for comparing selected regions of the C. elegans and C. briggsae genomes is now available.
April 12, 2003: ORFeome v1.1 data available
WormBase now contains the primer sequences and amplification results for 19,478 ORFeome v1.1 gateway clones, as described in Reboul et al. Nat. Genet. 2003 Apr 7. OST reads showing C. elegans gene structures in need of correction will be available in the near future. For now see WORFdb.
April 5, 2003: New Release Schedule
Effectively immediately, WormBase will be testing out a new release schedule. New releases will appear every two weeks, as before, but for one week preceding a release, a preview will be available at the WormBase development site. The WS98 release will appear on the development site on April 6, 2003, and will become available on the main site on April 13.
April 4, 2003: New WormBase server
We have just brought a new WormBase server online. It should provide noticeably improved performance over the old machine. The development server has been moved to dev.wormbase.org. Please let us know if you notice anything "unusual" about the new WormBase site.
March 24, 2003: Mug Winners Announced
Congratulations to the ten lucky winners from the user's survey random drawing. They will each be receiving a WormBase coffee mug!
February 25, 2003: WormBase Anonymous CVS Server up and Running
You can download up-to-date WormBase software directly from our Anonymous CVS repositorie s.
February 25, 2003: Web Site for International C. elegans Conference Open
The web site for the 14th International C. elegans Confer ence is now open. Deadline for abstracts is March 27, 2003 and for registration is May 30, 2003.
Textpresso Launch
Textpresso, a new search engine for the full text of C. elegans papers is now available. Individual sentences of over 1800 papers and 9000 abstracts are now searchable using keywords and term categories.
February 9, 2003: WS95 online
WormBase release WS95 is now available. See the change notes for a list of new and changed genes.
February 3, 2003: Ensembl gene predictions for C. briggsae available
The Ensembl project has published a new gene build for C. briggsae. The number of genes is about half the size of the canonical set because of Ensembl's conservative use of existing proteins to confirm genes, but these models are thought to be highly reliable.
January 26, 2003: New face for WormBase
The new banner and navigation bar designed for WormBase by Thomas Boulin has now been installed. Let us know what you think.
January 17, 2003: New RNAi data sets available
The results from the systematic RNAi screen reported in Kamath et al. Nature 421:231-237 (2003) are now available for browsing and bulk download. The results from the RNAi screen of ovary-enriched genes reported in Piano et al. Current Biology (2002) are available for browsing from the RNAi search page.
January 10, 2003: Scriptable access to the WormBase ACEDB
Server has been moved to aceserver.cshl.org, port 2005. The old port 2007 database running on www.wormbase.org has been disabled. Please see Direct Access to the Data for more information.
January 6, 2003: C. elegans Sequence Consortium wants your feedback
The Sequencing Consortium wants to know of any potential problems in the now contiguous six C. elegans chromosomes, for example, any evidence of deleted YACs, etc.. Please inform Alan Coulson (alan@sanger.ac.uk).
January 4, 2003: Gene page launch
A new gene page has been introduced to simplify WormBase navigation.