Genes2Diseases: predict genes associated to inherited disease.
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.
XplorMed: analyse the results of a query in MEDLINE.
Members of the group
- Miguel A. Andrade (May 2003) principal investigator
- Paul Krzyzanowski (Sep. 2004)
- Andrew Lysyk (Sep. 2005) coop student
- Enrique M. Muro (Jun. 2003)
- Gareth Palidwor (Jan. 2003)
- Carolina Perez-Iratxeta (Jul. 2003)
- Christopher J. Porter (Jan. 2003)
- Sergey Shcherbinin (Nov. 2003) external collaborator
Main subjects of research
- development of methods for the analysis of high-throughput genomics data, as produced from microarray, SAGE, and proteomics analysis;
- association of genes to human disease by analysis of biological databases; (data mining of biological information from databases of literature, sequence, human disease, etc.);
- development of tools for processing and viewing biological data, including phylogenetic trees, and sequence to sequence comparisons; and
- the application of Bioinformatics tools to particular experimental problems such as the analysis of concrete protein families or protein domains.
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.
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.
We are developing tools to analyse data from Serial Analysis of Gene Expression experiments and doing analysis of samples studied with this technique.
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.
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.
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.
As of November 2004 we have the following computing resources:
- Sun Fire V60x Compute Grid Rack System, with 41 x V60 servers, each with dual 3.06 GHz Intel Xeon CPUs, 2 GB memory and dual 36 GB SCSI disks.
- 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.
Last modified 2005-11-21 02:08 PM