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Ontario Genomics Innovation Centre

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Bioinformatics Research

The Bioinformatics group of the Ontario Genomics Innovation Centre is pursuing research activities in a variety of subjects regarding the analysis of gene and protein function using computational algorithms and database information. The results of our research are made available to the scientific community via software distribution and as web services.

BiasViz: represent amino acid bias in protein sequences from an alignment.

Genes2Diseases: predict genes associated to inherited disease.

K2D2: predict protein secondary structure content from circular dichroism spectra.

Marker Server: discover marker genes in sets of gene expression data. Currently you can examine a set of 80+ murine stem cell related samples.

PhyloView: colour a phylogenetic tree according to taxonomy.

Probe2GO: obtain extended GO annotations for Affymetrix probe sets. 

StemBase: explore a database of gene expression data from stem cell samples.

Transcriptome Sailor: examine a genomic region in mouse or human for 3' transcript ends according to EST evidence.

XplorMed: analyse the results of a query in MEDLINE.

Training

As part of our collaborations with and support of OHRI and Stem Cell Network researchers we provide training in Bioinformatics, microarrays and data analysis. We have developed an online course for the Stem Cell Network on the analysis of microarrays.

Members of the group

Former members and visitors

Main subjects of research

  1. development of methods for the analysis of high-throughput genomics data, as produced from microarray, SAGE, and proteomics analysis;
  2. association of genes to human disease by analysis of biological databases; (data mining of biological information from databases of literature, sequence, human disease, etc.);
  3. development of tools for processing and viewing biological data, including phylogenetic trees, and sequence to sequence comparisons; and
  4. the application of Bioinformatics tools to particular experimental problems such as the analysis of concrete protein families or protein domains.

Projects

LIMS

The group is developing and implementing tools to track samples and results from the core facility, and to distribute results to users within and outside the OHRI.

Affymetrix

We provide assistance with the analysis of Affymetrix GeneChip experiments, and have written tools to perform custom analysis of data from expression and mapping chips. We will provide help with the use of commercial and free analysis tools as they are acquired, and can assist with custom annotation of results.

SAGE

We are developing tools to analyse data from Serial Analysis of Gene Expression experiments and doing analysis of samples studied with this technique.

StemBase

We are developing a comprehensive database from the results of Affymetrix, SAGE, and proteomics analysis of stem cell samples. This database is being mined to determine gene expression patterns typical of stem cells, and changes in gene expression that occur in stem cell differentiation.

Tools

We are using standard bioinformatics tools, such as BLAST, FastA, ClustalW, HMMER, and the EMBOSS suite, to analyse the data produced in the OGIC. We are examining approaches to make them generally available to users in the OGIC, and ultimately throughout the OHRI. As part of this process we maintain up-to-date copies of major sequence, structure, and pathway databases.

Other Projects

We are eager to explore possibilities for collaboration, or to provide bioinformatics services in the context of new grants. Please contact Miguel Andrade if you are interested.

Computer Hardware

As of July 2006 we have the following computing resources:

  • Sun Fire V60x Compute Grid Rack System, with 41 x V60x servers, each with dual 3.06 GHz Intel Xeon CPUs, 2 GB memory and dual 36 GB SCSI disks.
  • 8 x2100 compute nodes used for with ThermElectron Sequest BioWorks proteomics software.
  • Sun Fire V480 database server with 4 UltraSPARC III 1.05 GHz processors, 8GB shared memory, dual 73 GB SATA disks with 8MB cache, and a Sun StorEdge 3311 disk array with 12 x 250 GB SATA disks.
  • File server with a Sun StorEdge 3310 disk array with 12 x 73 GB Ultra160 SCSI disks, using single RAID controllers with 512 MB cache.
  • Two backup servers, dual 2.4 GHz Intel Xeon CPUs with 1 TB disk space.
  • Several desktop machines running Linux, Solaris, MacOS X and Windows 2000

Our cluster has a TPP (Theoretical Peak Performance) of 506 GFLOPS, and a total of 86 GB of distributed memory, 8 GB of shared memory, and 8 TB of hard disk storage capacity.

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Last modified 2008-04-23 07:41 AM