WormBase Development

Development site offline

Todd Harris (harris@cshl.edu) — Mon, 10 Sep 2007 10:22:12 -0700

The development site will likely be offline for most of today and tomorrow while we sort out multiple problems with the GFF databases for WS180 and WS181.

Intermittent outtages on development server

Todd Harris (harris@cshl.edu) — Tue, 30 Jan 2007 10:27:15 -0700

The development server may be offline intermittently today. I'm rebuilding the GFF databases for WS170. Due to a severe disk space shortage, I may have to remove the old database first, in effect bringing the site down. It should be back up reliably later this afternoon.

WS155 now available for testing on the development site

Todd Harris (harris@cshl.edu) — Mon, 13 Mar 2006 13:43:41 -0700

I've just finished rebuilding WS155 with the new release provided by Anthony. As usual, your testing of the development site is appreciated!

WS154 patches: fosmid coords, CDSs

Todd Harris (harris@cshl.edu) — Thu, 02 Mar 2006 08:26:25 -0700

Michael and I have been working on several fixes for WS150 and WS154:

1. I have patched the genetic mappings for fosmids in WS154, as some people noticed that the genetic coordinates was based on clone coordinates instead of chromosomes.
The patch will be available soon from ftp.wormbase.org

2. Kris Gunsalus pointed out that some transcripts are connected to wrong cds'es in the GFF files of the frozen releases. In addition we found that some UTR lines are missing.
As this messed up the GBrowse display of that regions and seems to have caused problems since a long time, we fixed it for WS154 as well as the last frozen release WS150.
Because of this it might be necessary to download the updated GFFs from ftp.wormbase.org if you are using a local GBrowse or the five_prime_UTR and three_prime_UTR lines from the GFFs or have problems with the annotation of CDS<->transcript in the coding_exons of chromosome IV,V and X GFF files.

No coordinates were changed, just missing UTR exons were added in cases were an exon contained both UTRs aa well as the CDS. And as mentioned before some description fields contain now the correct CDS/Transcript.

I marked the change to the frozen WS150 release in the WiKi at "http://www.wormbase.org/wiki/index.php/WS150#Database_issues_.2F_patches"

Please be aware that all frozen releases before WS150 were and will not be fixed.

BLAST out on the main site

Todd Harris (harris@cshl.edu) — Mon, 13 Feb 2006 11:09:54 -0700

BLAST/BLAT services are out on the main site. The problem looks to be associated with inadvertent syncing of some 3rd party libraries (Gbrowse) that require a Perl ugrade. Now upgrading Perl to 5.8.8 and should have service restored shortly.

Development Site updated to WS154

Todd Harris (harris@cshl.edu) — Fri, 10 Feb 2006 14:18:41 -0700

The development server has been updated to WS154. WS153 will be moved to the production servers later this evening.

Strain search now handles genes and variations

Todd Harris (harris@cshl.edu) — Tue, 07 Feb 2006 18:17:12 -0700

The Strain search formerly required a strain ID. Now it accepts genes and variations as well. This makes it very easy to find, say, all strains carrying a specific allele. For example, the following link displays all alleles carrying unc-26(e205).

http://dev.wormbase.org/db/gene/strain?name=e205

WormBaseWiki (beta) now available

Todd Harris (harris@cshl.edu) — Sat, 04 Feb 2006 12:06:49 -0700

I'm now nearly finished setting up and configuring MediaWiki. For the time being the Wiki is running on crestone.cshl.edu and is available at www.wormbase.org/wiki

Google indexing of dynamic content

Todd Harris (harris@cshl.edu) — Sat, 04 Feb 2006 10:47:34 -0700

I have recently opened up dynamically created pages at WormBase to Google indexing. This is something we have avoided in the past because of inherent problems with server load.

After just a few days, there are now over 300K results for WormBase in google! (Note: not all of these URLs have been indexed yet).

Searches also work quite well (eg endosome) although I'm a little hesitant about relying on results since the entire database hasn't been indexed. Still, this should provide a quick entry point for current users, as well as draw in additional traffic from other researchers.

Development Site updated to WS148

Todd Harris (harris@cshl.edu) — Tue, 13 Sep 2005 10:48:19 -0700

WormBase has been updated to the WS148 release of the database. This release includes new expression cluster data.

Upcoming service interruption - 26 Aug 2005

Todd Harris (harris@cshl.edu) — Wed, 24 Aug 2005 10:49:35 -0700

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.

WormMart has been updated to WS145

Todd Harris (harris@cshl.edu) — Sun, 19 Jun 2005 10:51:09 -0700

WormBase has been updated to the WS145 release of the database. Development for this release focuses on tweaks to handlingof the Variation and Gene_name class.

Genes now searchable by RefSeq and AceView IDs

Todd Harris (harris@cshl.edu) — Sat, 07 May 2005 10:52:45 -0700

It is now possible to search for genes using NCBI RefSeq (NM_058274) or AceView identifiers (XC24).

Protein motifs now displayed on the Genome Browser

Todd Harris (harris@cshl.edu) — Thu, 24 Mar 2005 10:53:48 -0700

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.

Public beta of WormMart, a new data mining facility

Todd Harris (harris@cshl.edu) — Tue, 22 Feb 2005 10:54:35 -0700

WormBase is pleased to announce WormMart, a new data mining facility now available for public beta testing. The WormBase implementation of Biomart was built by Will Spooner. You can read more about the public beta test of WormMart at:

http://dev.wormbase.org/about/wormmart.html