Sources at Google have disclosed that the humble domain, http://research.google.com, will soon provide a home for terabytes of open-source scientific datasets. See: http://blog.wired.com/wiredscience/2008/01/google-to-provi.html

Here's the PDF of the poster I presented at the CSH Rat Genome meeting earlier in December. It includes an overview of the user interface and what each option can be used for, along with some example analyses:

1. Gimap region of RNO4 showing identification of informative SNPs between a group of strains.
2. Analysis of LEXF x FXLE recombinant inbred lines in the region of a Cholesterol level QTL on RNO5
3. Hypertensive vs Normotensive strains across a region of RNO5 associated with many hypertension QTL.

Rat Genomics and Models 2007 meeting was held on December 6-9 at Cold Spring Harbor. Many people from HMGC, including RGD attended the meeting and presented in talks or posters. I have attached the poster I presented on pathway data at RGD - the development and structure of the Pathway Ontology (PW), the annotations of targeted pathways in conjunction with the Disease Portals and across three species (rat, human, moluse), possible future collaborations.

The talks and abstracts and the photo gallery can be viewed, upon registration, at:

http://leadingstrand.cshl.edu/

"Poster SJL 12-5-07.ppt" was presented at the meeting. "Poster SJL 11-8-07.ppt" is a preliminary version featuring "the trashcan".

We have a proof of concept Flex ( aka Adobe Flash ) Ontology browser at:

http://labs.rgd.mcw.edu/ontology/browse.html

Jeff De Pons created this to test if flex could handle displaying all our ontology trees. It only lets you double click on nodes and drill down each ontology tree and back up again.

As part of the demo we're doing at the Cold Spring Harbor rat meeting this year, I've created a brief tutorial/walk through of some of the tools on RGD for use in the afternoon demo session. You can download the PDF document and then follow the instructions to take a brief guided tour of some of the RGD features. It covers basic searching, using the ontologies and GViewer to search in more specific ways and then finishes with QTLs and finding and downloading cell cycle genes in a QTL region.

We have a demo of our newly redesigned RGD site up and running at http://rgddev.mcw.edu. It will be avalable untill Dec 14th 2007.

I've just finished an enhancement to the SNPlotyper tool that connects the application up to the R statistical package so it can use hierarchical clustering to order the strains. This means that you can define a region, select the strains you wish to analyze and then use the clustering option to group the strains based on similar genotype across the region. You can still manually order the strains as before by using the drag and drop feature on the main SNPlotyper form.

Latest Screen Shot of new Web site redesign.