Large Scale Genome Analysis and Hardware Provision

Led by Dr. Christoph Sensen

Computational infrastructure

The Bioinformatics innovation Centre provides computational infrastructure support through hardware and database resources.

The lead site for the Bioinformatics Innovation Centre is located at the Sun Centre of Excellence for Visual Genomics (COE) at the University of Calgary’s Faculty of Medicine. As the foundation of hardware service provision for the Innovation Centre, the COE built a Bioinformatics Grid that connects its hardware components and provides the following:

• Generic login capability to over 1,500 users across Canada. This service is free of charge for Canadian researchers from academic institutions.
  
  
• Access to dedicated search engines with approximately 5,000 field programmable gate array (FPGA) CPUs.
  
  
• Data storage (over 200 Terraabytes of hard disk and tape-based storage).
  

Software tools and databases

The Innovation Centre offers over 1,000 software tools, access to dozens of locally mirrored databanks, and compute power dedicated to Bioinformatics including Canada's only TimeLogic Decypher database search engines, as well as the world’s first Java 3DTM-enabled CAVE automated virtual reality environment. Generic users of the Bioinformatics Innovation Centre have access to software tools and databases, including:

MAGPIE -- A software system for automated analysis, annotation, and presentation of DNA and protein sequences. For any gene or feature of interest in a given genome, MAGPIE presents a comprehensive visual summary of matching sequences found in many of the known genomic and proteomic databases, ranked by similarity. These summaries provide rich evidence to users wishing to interpret a gene’s biological roles and origins. MAGPIE distills results of multiple database searches for each sequence (e.g. Expressed Sequence Tags [ESTs]) or subsequence (e.g. Open Reading Frames [ORFs] in bacterial genomic DNA) into a visual summary page that users can further curate.

Bluejay -- A portable browser for visual analysis of genomes. Bluejay allows users to visualize complete genomes, explore the functional annotation of all genes, and display gene activity as an animated time series. Other features include the ability to create a personalized account, links to MAGPIE annotation pages for all genes, and support of BioMOBY web services. Bluejay is written in Java and therefore platform-independent, as well as available from the website and as a downloadable version.

TimeLogic Decypher Web Interface -- An accelerator platform for high-throughput bioinformatics database searches. Using field-programmable gate arrays (FPGA), it performs highly sensitive sequence similarity searches such as the various types of Hidden Markov Model (HMM) or Smith-Waterman analyses that would otherwise be too large for public resources and too time-consuming for local computer clusters.

BioView Workbench -- A high-throughput accelerator for biological sequence similarity searches and genomic sequence annotations. The Workbench allows users to deploy highly sensitive algorithms for sequence comparison such as the Smith-Waterman algorithms, with speedups of hundreds or even thousands of times compared to regular computer installations. The Workbench has a web-based interface for submitting searches, performing genomic sequence annotation, and displaying results graphically.

BioMOBY-- The MOBY-S system defines an ontology-based messaging standard through which a client is able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next.