RECOMB meeting on system biology and reverse engineering was held at MIT, Cambridge, MA in the fall of 2008. The poster was showing the various features of the interactive diagrams that we started publishing in the spring of 2008. One particular feature of the diagrams is that other pathways that are triggered by the pathway the diagram depicts can be accessed offering users the ability to 'walk' from one diagram to another and explore pathway connectivity. The feature exploits the availability of the ontology and the resources of the Pathway Studio software from Ariadne Genomics.

The Biology of Genomes May 2008 meeting was held at CSHL. The poster, in addition to presenting the ontology and annotations, was showing a few of the interactive pathway diagrams that we started publishing in the spring of 2008 using the Pathway Studio software from Ariadne Genomics in conjunction with a CMS (Content Management System).

RGD is developing a database to house detailed phenotype data derived from both large-scale and small-scale phenotyping projects. The data currently includes a subset of the results from the PhysGen Programs for Genomic Applications at MCW and Japan’s NBRP. Click the link below to try out a prototype of the data mining tool designed to access, explore and retrieve this data.

http://rgd.mcw.edu/rgdweb/

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, mouse), 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.