Chinook's usage in the Sockeye 3D Genome Browser

Sockeye is a comparative genomics browser that was developed at the BC Genome Sciences Centre in 2003. It was designed to allow users to manipulate and observe genomic annotation across multiple genomes, with the specific aim of aiding in the elucidation of transcription factors. To enable users to access, a wide variety of established bioinformatics tools for phylogenetic footprinting, motif discovery/scanning, and primer prediction, the Chinook project was embarked on. Chinook aimed to provide Sockeye with a rich and diverse set of bioinformatics utilities. It soon became apparent, that instead of following in the footsteps of other projects that somehow linked their application to bioinformatics utilities, we could create a ubiquitous, distributed framework for integrating this functionality into all advanced genomics applications. For instance, multiple projects could take advantage of the integration efforts of individual users using Chinook; if a user was adding Clustalw, Lagan, Genscan, or any other program to Sockeye via Chinook, they would actually be making this service available to all the applications that use Chinook. It is strongly felt that this would capture the current state-of-the-art in bioinformatics, and allow for richer, more competitive comparisons of the available algorithms.

Below are some screenshots of Chinook being used in Sockeye

Selecting alignment regions in Sockeye

Chinook loading in Sockeye

Discovering services with Chinook

Selecting an alignment algorithm from Chinook

Entering parameters in Chinook

Job Submission via Chinook

Final results in Sockeye