WormBase News Archive: 2005

October 26, 2005: New release of WormBase, WS149
WormBase has been updated to the WS149 release of the database. This release includes over 20,000 new oligo set microarray probes from Agilent and updated blast databases of human and Drosophila.
October 17, 2005: Cell-Specific microarray data now available in WormBase
A profile of embryonic unc-4::GFP motor neurons generated using MAPCeL (MicroArray Profiling C. elegans cells) from Fox, et.al, 2005 is now available in WormBase. Gene lists for both enriched and expressed genes can be accessed from Expression Cluster and Gene report pages (e.g. alt-1).
October 7, 2005: Possible WormBase Access Interruption
Due to a dispute between two major ISPs, the WormBase web site may not be accessible to certain Internet users until the dispute is resolved. We apologize for what we hope will be a very temporary inconvenience. For more information, please see: http://ask.slashdot.org/article.pl?sid=05/10/05/2247207&tid=95&tid=187&tid=4.
October 2, 2005: New WormBook chapters available
Chapters recently added to WormBook include: Genetic enhancers, Genomic classification of protein-coding gene families, Alternative splicing in C. elegans, C. elegans microRNAs, Cell cycle regulation, Mitochondrial genetics, Gastrulation in C. elegans. For a monthly email containing information about new additions to WormBook, please sign up at http://www.wormbook.org/announce.html.
September 30, 2005: Intellectual lineage images now available
Images of the C. elegans community intellectual lineage displayed at the International Worm Meeting this summer are now available for download.
September 29, 2005: New release of WormBase, WS148
WormBase has been updated to the WS148 release of the database.
September 26, 2005: GSA Model Organisms Meeting
The Genetics Society of America is having their first meeting focusing on model organisms: Genetic Analysis: Model Organisms to Human Biology, January 5-7, 2006. The Abstract deadline is November 14. Additional information and registration is available at www.gsa-modelorganisms.org.
September 20, 2005: Summer 2006 C. elegans Topics Meetings announced
Instead of multiple regional meetings in North America, two topics meetings will be held at the University of Wisconsin at Madison in 2006. If this format works well four topics meeting will be held in 2008. The 2007 International Meeting will be held at UCLA.
June 22rd-25th, 2006
Meeting 1: Early Embryo, Polarity & Cell Fate, Post Embryonic Development, Cell Biology & Cell Cycle, and Germline/Evolution/Sex Determination (Organizers: Ahna Skop, Jeff Hardin and others)
July 9-July 12th
Meeting 2: Behavior and Sensory Transduction, Neuronal Development, and Synaptic Function (Organizers: Maureen Barr, Ahna Skop and others).

Meeting 3 (Genomics, RNAi, & Gene Expression) and Meeting 4 (Aging and Stress, Dauer and Developmental Timing, Cell Death & Neurodegeneration, and Pathogenesis) will be added in 2008. If anyone is interested in helping Ahna Skop organize one of the 2006 meetings please contact her at: skop@wisc.edu.
September 19, 2005: Preliminary C. remanei genome browser now available
A browsable view of the C. remanei genome is now available. Analyses include a variety of gene model predictions, protein and EST alignments, and nucleotide-level alignments to C. elegans and C. briggsae. These data are based on a preliminary assembly of the genome; users are urged to treat this data in accord with its pre-release status.
September 13, 2005: New WormBook chapters available
Recent additions to WormBook include: Introduction to genetics and genomics, Basement membranes, Introduction to the germ line, Germline proliferation and its control, Introduction to signal transduction, TGF-beta signaling, GABA, Introduction to nematode evolution and ecology, Nematode genome evolution, and Interactions with microbial pathogens.
September 12, 2005: 2006 European Worm Meeting web site now available
The web site for the European Worm Meeting 2006 is online at www.imbb.forth.gr/ewm2006/. Organizer: Nektarios Tavernarakis (Greece). Organizing Committee: Christian Eckmann (Germany), Monica Gotta (Switzerland), Neil Hopper (UK), Fritz Muller (Switzerland), Stephen Nurrish (UK) Francesca Palladino (France), Jerome Reboul (France), Peter Swoboda (Sweden).
Upcoming Service Interruption: August 26, 2005
Due to scheduled maintenance and performance upgrade, WormBase will be unavailable starting at 5 PM EDT (UTC -4). We hope to have service restored by 9 PM. Should you require access during this period, consult our list of mirrors at the bottom of this page or use the development site.

Service to the site was restored at 6:45 PM EDT but intermittent outtages may persist until domain name server entries have propagated across the globe.

We apologize for any inconvenience this interruption may have caused.
August 22, 2005: Variations now available through WormMart
Variations, including alleles and SNPs, are now available for downloading en masse via the WormMart.
August 21, 2005: First published reference of C. elegans
The first published reference to C. elegans -- the paper that describes C. elegans as a new species -- is now available at WormBase [PDF]. This translation and an accompanying foreword [PDF, DOC] have been kindly provided by Marie-Anne Felix.
August 21, 2005: New release of WormBase, WS146
WormBase has been updated to the WS146 release of the database. This release contains over 1000 new curated expression patterns, many with accompanying images. See ZK430.2 for an example.
August 3, 2005: New release of WormBase, WS145
WormBase has been updated to the WS145 release of the database which includes updated alignments to the latest human IPI protein set.
August 2, 2005: Initial WormBook chapters now available
The first 90 chapters of WormBook are now available as preprints.
July 25, 2005: RNAi datasets now available
A mapping table of Julie Ahringer RNAi clones to current predicted genes is now available in a flat file format. The Ahringer RNAi feeding library uses GenePairs names to label bacterial strains. GenePairs names usually, but not always correspond to predicted C. elegans gene names. The mapping file reconciles these discrepancies and also contains some additional information including clone plate location, clone error report status and type of affected gene. The file is synchronized with the current live release to provide up-to-date mapping information. A link to the mapping file can be found in the Worm Reagents section of the main page (listed as RNAi clone mapping).
July 18, 2005: European Worm Meeting announced
The 2006 European Worm Meeting will take place in Hersonissos, Crete, Greece, between the 29th of April and the 3rd of May. The Organizer: Nektarios Tavernarakis (Greece). The Organizing Committee consists of: Christian Eckmann (Germany), Monica Gotta (Switzerland), Neil Hopper (UK), Fritz Muller (Switzerland), Stephen Nurrish (UK), Francesca Palladino (France), Jerome Reboul (France) and Peter Swoboda (Sweden). Additional details will be posted here when available.
June 21, 2005: WormBase Position at Caltech
WormBase/Caltech has an open position for a Biological Curator. Please contact Paul Sternberg (pws@caltech.edu) for information.
June 19, 2005: New Release of WormBase, WS144
WormBase has been updated to the WS144 release of the database. This release includes updated versions of Uniprot BLASTP and BLASTX analyses.
June 16, 2005: Two additional nematode genomes in sequencing pipeline
Two additional nematode genomes are now in the sequencing pipeline. Heterorhabditis bacteriophora, an entomopathogenic nematode used in insect control, has been approved for sequencing by NHGRI but not yet assigned to a sequencing center. Haemonchus contortus, an economically important sheep and goat nematode parasite, is currently being sequenced at the Wellcome Trust Sanger Institute. These additions will bring the total number of sequenced nematode genomes to ten in the near future.
June 9, 2005: First set of gene interaction data available
WormBase has added ~4000 (some redundant) genetic and regulatory interactions to the database. These interactions were extracted from the C. elegans literature using Textpresso. Interactions are available on the Gene Summary pages. Please send us your comments and corrections.
June 6, 2005: WormBase Position at Wellcome Trust Sanger Institute
WormBase/Sanger has an open position for a Computer Biologist. Please see the full job description for additional details.
June 2, 2005: Textpresso on "autopilot"
The worm literature search, powered by Textpresso , is now updated weekly with newly published papers and additional classic papers.
May 30, 2005: New Release of WormBase, WS143
WormBase has been updated to the WS143 release of the database. This release includes the first set of curated gene interaction data. See cdf-1 for an example.
May 8, 2005: Gene page now searchable by NCBI RefSeq, AceView IDs
The Gene Summary page is now searchable by RefSeq and AceView IDs (such as RefSeq: NM_058274 and AceView: XC24). Read more about AceView and RefSeq at NCBI.
May 8, 2005: New release of WormBase, WS142
WormBase has been updated to the WS142 release of the database. Among the improvements in the WS142 release are revisions to the Gene Summary page to enhance performance and site-wide revised handling of Gene Ontology terms.
April 29, 2005: WS140 date freeze website now available
The WS140 data freeze website is now available at ws140.wormbase.org. It will be available in perpetuity at this URL. Raw files for the WS140 release can be obtained from the WormBase FTP site. We encourage all users conducting bioinformatic analyses to use the most recent "frozen" release of the data.
April 27, 2005: Batch Genes still available
Although we have recently replaced the link to "Batch Genes" in the main navigation bar with one to WormMart, Batch Genes will continue to be available. Links to Batch Genes will be found in the Web Site directory on this page and in the Site Map.
April 26, 2005: Fire Lab Vector Kit available at AddGene
The Fire Lab C. Elegans Vector Kit is now available for distribution to scientists at academic and non-profit institutions through Addgene. This kit contains 288 vectors lacZ and/or GFP fusion vectors for studying gene expression, control plasmids for RNA-mediated interference, vectors for bacterial-mediated RNAi, and much more. Addgene is a new not-for-profit research support service dedicated to archiving and distributing plasmids from published articles. More information on the kit is available on the AddGene site.
April 23, 2005: Introducing WormMart
WormBase is pleased to announce the public release of WormMart , our implementation of the BioMart project. WormMart is intended as an eventual replacement for the "Batch Genes" and "Batch Sequences" pages. These pages will continue to be available, linked through the Site Map and the website directory. Learn more about how to use WormMart.
April 20, 2005: White paper for model organisms ENCODE project
A white paper [text, .doc] is being submitted to NHGRI to argue for the creation of a model organism analog of the human ENCODE (ENCyclopedia of DNA Elements) project and for the inclusion of C. elegans in that effort. The white paper will be submitted on Monday, April 25, 2005. Please send any suggestions or comments to worm_encode_goffer@gs.washington.edu. See the human ENCODE project for reference.
April 19, 2005: New release of WormBase, WS141
WormBase has been updated to the WS141 release of the database. The WS142 release of the database is now available for testing on the development site.
April 11, 2005: Protein motifs now displayed on the Genome Browser
Protein motifs are now displayed in genomic coordinates on the Genome Browser. You can see these features by enabling the "Protein Motifs" track. This track was created by interpolating translated coordinates of protein motifs into genomic coordinates. In the event that a motif spans an exon boundary, a dashed line is displayed.
April 8, 2005: First WormBase mirror site in Asia now available; all mirrors stabilized
The third WormBase mirror site -- and our first in Asia -- is now available at wormbase.ccbb.re.kr. The mirror is hosted at the Center for Computational Biology and Bioinformatics in Daejeon, South Korea and maintained by Chang Hyuk Kwon. This site joins our two existing mirrors at Caltech (Pasadena, CA USA) and IMBB (Crete, Greece). We have also established a robust mechanism for keeping these sites up-to-date. If you are interested in hosting a mirror in your lab or at your university, please contact Todd Harris (harris@cshl.edu).
April 5, 2005: New genome-wide RNAi screen on early embryogenesis is now available
The results from the systematic RNAi screen reported in Soennichsen et al., "Full genome RNAi profiling of early embryogenesis in C. elegans" are now available on the development site. There are links to movies and other relevant information at the PhenoBank. See WBRNAi00049552 for an example.
March 26, 2005: New release of WormBase, WS140
WormBase has been updated to the WS140 release of the database. New features include the introduction of a unified Variation class, which consolidates all information on alleles and polymorphisms into a single class. To support this class, the Locus and Allele/Variation displays have been overhauled. WS140 will be a "frozen" release of the data and software, permanently available at ws140.wormbase.org in three weeks.
March 21, 2005: WormBase literature search updated
A number of improvements have been made to the WormBase Literature search engine in line with the new Textpresso build release. The full text of over 1,000 new journal articles pertaining to worm biology have been added to the database; four new search categories are available from the drop down menus; minor improvements have been made to the interface, including a new sort function.
March 9, 2005: Public beta test of WormMart
WormBase is pleased to announce WormMart, a new data mining facility now available for public beta testing. Read more about WormMart and the public beta test.
March 4, 2005: New release of WormBase, WS139
WormBase has been updated to the WS139 release of the database.
February 27, 2005: New commercial microarrays from Agilent
Agilent has released a new C. elegans 22K oligo microarray with sequences from WS129. Additional information is available on the product page at Agilent's website.
February 11, 2005: New release of WormBase, WS138
WormBase has been updated to the WS138 release of the database. New features in this release include the use of controlled vocabulary anatomy ontology terms in association with expression patterns. A prototype search for expression patterns using these terms will be available next week.
February 7, 2005: 15th International C. elegans Meeting website now available
The Fifteenth International C. elegans Meeting will be held at the University of California at Los Angeles June 25 (Saturday) - June 29 (Wednesday), 2005. Abstracts are due March 22. Please request new gene names prior to submitting your abstracts!
January 21, 2005: Upcoming scheduled service outtage
WormBase will be offline on Tuesday, January 25th from approximately 5:30 PM to 10:30 PM EST for scheduled hardware maintenance. We apologize for any inconvenience. Users may wish to use the Caltech WormBase mirror site during this period.
January 20, 2005: New release of WormBase, WS137
WormBase has been updated to the WS137 release of the database.
January 13, 2005: New Gene Class display
A new Gene Class display summarizes information on three- and four- letter gene classes. Entering a specific class such as unc or egl displays all genes associated with that class.

WormBase News Archive: Jan 2005-to-date