brie6, aceserver, blast, gene, crestone, and vab have all been updated to the WS155 release of the database. I need to remove some apparent debugging statements in the check_disk_space() methods of Bio::WormBase…
I’m almost done putting the finishing touches on a new Genetic Map display. Intended as a drop-in replacement for the Acedb GMap, the new Genetic Map leverages the GBrowse infrastructure providing a familiar user interface as that for browsing the genome.
I still need to fix a few small things (what in the hell is a centi-centi-Morgan?) 🙂 RD also asked if it might be possible to display mapping data. I think some small modifications of my code that I use for calculating confidence intervals should be sufficient for generating spans for both 2- and 3- factor crosses. The display might get a little complicated displaying separate spans for each experiment – it might be better to aggregate like-experiments together?
I’ve made a huge number of changes under the hood to make the update process simpler and more stable. A number of things precipitated these changes, including the rapidly expanding size of the database, increasing number of denormalized support databases, the need to run the site in a load balancing situation — and most importantly, the looming addition of 3 new species sometime this year.
I’ve refactored the old Bio::GMOD modules into its own namespace — Bio::WormBase — in part to avoid possible future namespace conflicts as well as too allow a degree of flexibility not present in the old modules.
– Resumable downloads (no longer limited to the Net::FTP/Perl 2GB limit of some architectures).
– purging of old releases
– versioning of all mysql databases, etc, etc, etc
– consolidation and versioning of blast, blat, and epcr databases
– Service monitoring and restarting as necessary (underway)
You can check out these new modules from sourceforge. I would encourage all of you to become sourceforge developers if you aren’t already so that we can work together to make the mirroring process as streamlined as possible. Please contact me so that I can add you to the list of developers. The project name is bio-wormbase, and the first module is Bio-WormBase.pm. I plan on adding a bunch of other things, such as data mining examples, adminstrative scripts, etc.
Thanks for all your help!
The following documentation is copy-pasted from our Wiki where it is a little easier to read
Fetching the new modules:
cvs -d:pserver:firstname.lastname@example.org:/cvsroot/bio-wormbase login
cvs -z3 -d:pserver:email@example.com:/cvsroot/bio-wormbase co -P Bio-WormBase.pm
cvs -z3 -d:ext:firstname.lastname@example.org:/cvsroot/bio-wormbase co -P Bio-WormBase.pm