New VC2010 and improved CB4856 genomes published

The VC2010 genome assembly has just been published in Genome Research as an open-access article. This assembly is largely derived from a completely isogenic VC2010-derived strain, PD1074, that is now available from the CGC.

In related news, Junho Lee and his lab have simultaneously published an open-access article on their substantially improved genome assembly for Hawaiian C. elegans (CB4856).

UC Davis features micropublications publishes brief, novel findings, negative and/or reproduced results, and results which may lack a broader scientific narrative. Each article is peer reviewed and assigned a DOI. Included data is curated and, upon publication, deposited in third party referential databases (when available).

Recently UC Davis featured an article, ‘Small Science Snippets: Micropubs Help Share Discoveries‘ about how one of their researchers used a micropublication to publish their results.

Micropublish your results today!

SGD turns 25!

25 years ago the SGD (The Saccharomyces Genome Database) went online.  Happy Birthday SGD!

SGD provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.

WormBase collaborates with SGD and several other model organism databases to facilitate data harmonization and cross-species searches at the Alliance of Genome Resources.  Check it out!

Short WormBase downtime yesterday

WormBase went down at 2.54pm ET yesterday. The problem was caused ironically by a fault recovery mechanism that was introduced recently. The fault recovery mechanism takes faulty servers out of service and replaces them with healthy ones. The process involves two components:the detection of faulty servers and the creation of new ones.

Two simultaneous problems in the two components lead to the failure. A false positive in detecting the faulty server caused the sever to be taken out of service, and a missing hard drive snapshot caused the failure to start new servers.

To avoid such future occurrences we are looking into ways to make the fault detection more specific and prevent important disk snapshots from being deleted by automated processes.

Most of the web services were restored around 5 pm ET. Apologies for any inconvenience caused.