News

Nature Precedings, "a platform for sharing new and preliminary findings with colleagues on a global scale," has published a short article by Gramene staff scientist Charles Chen entitled "The Gramene Genetic Diversity Module: a resource for genotype-phenotype association analysis in grass species".

Apply for the travel awards to attend Gene Annotation Workshop to be held at the ASPB's Plant Biology 2010 meeting.

If selected, the travel award will cover the cost of your registration for the entire Plant Biology 2010 meeting. We expect to award 10-20 participants.

The Department of Crop & Soil Science at Oregon State University seeks a scientist with strong traditional and molecular plant breeding knowledge and experience to lead a dynamic wheat variety and germplasm development team.

This is a 12-month, 1.0 FTE tenure-track position available at the assistant, associate or full professor level, tenure possible with the latter, depending on candidate experience. For a position description and application procedures, see http://oregonstate.edu/jobs    (posting number 0005761).

In collaboration with Ensembl Genomes, Gramene announces an interim update to our 31st build as follows:

• Updated A. thaliana variation database including data from Norborg GWAS, 1001 Genomes Project and WTCHG
• Updated O. sativa japonica variation database including OryzaSNP data
• Updated V. vinifera variation database for new assembly
• Updated BioMart

Also included is a software update from Ensembl version 57 to 58 that provides the following:

Gramene is please to contribute to the Plant Genome Resources exhibition booth at the upcoming Plant Biology 2010 meeting July 31 - August 3.

Gramene users may be interested in the 5th International Rosaceae Genomics Conference in Cape Town, South Africa, November 14-17, 2010. For full conference details, see the RCG5 website.

US residents and researchers may apply for travel awards to attend a Gene Annotation Workshop to be held at the ASPB's Plant Biology 2010 meeting (July 31 - August 4, 2010, Montreal, Canada). If selected, the travel award will cover the cost of the Plant Biology 2010 meeting registration cost. We expect to award 10-20 participants for the "Plant Ontology and Gramene's Gene Annotation Workshop" to be held on Saturday, July 31, 2010 from 8:00 AM to 12:00 PM.

Release #31 of Gramene brought new data sets and features in the Genetic Diversity module. Gramene Diversity now features five large-scale SNP genotype data sets generated by recent re-sequncing projects in rice, maize, and Arabidopsis from the OryzaSNP, Panzea, Arabidopsis 2010 and 1001 Genomes projects.

Genome sequencing continues to become less expensive and faster which is great news for researchers; however, manipulating and storing vast amounts of sequence data has become a challenge. Version 4.0 of the Genomic Diversity and Phenotype Data Model (GDPDM) database schema has a solution. Instead of storing individual SNP values, the 4.x version stores long haplotypes as Binary Large OBjects (BLOBs). Each SNP value only requires four bits of memory. Additionally, BLOBs are used to store physical positions and indel lengths. Version 4.1 added another BLOB to store SNP id values.

A while ago, Gramene instantiated a Distributed Annotation System (DAS) for serving some of our rice genome annotations directly from our markers and sequences database. We soon found that the size and design of our database was not optimized for type of real-time queries necessary to serve DAS.