Phone: [1] 403 220-4301 | Fax: [1] 403 210-9399 | E-mail: csensen@ucalgary.ca
This Web Site is updated infrequently. To get a better idea about current activities, please have a look at the Publications.
My laboratory is now working on the creation of 4D (spatial and temporal) systems for genome annotation and the visualization of genomic knowledge. To build the infrastructure for this research, we have collaborated with Sun Microsystems and Fakespace Systems to build a high-performance computing environment, including a Java 3DTM enabled CAVE (CAVE is a recursive acronym. It stands for CAVE Automated Virtual Environment).
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picture by Maja Swannie
The image below shows the layout of the CAVE
A Technical White Paper about our CAVE installation is now available in PDF format. Click here to go to the white paper.
We have created a middleware system called JABIRU, which allows us to manipulate Java 3DTM objects using the magic wand in the CAVE or keyboard and mouse on the standard computer. This allows users of our virtual reality models to work with complex data sets without the need for programming. Details about JABIRU can be found at the JABIRU Website.
Picture by Masumi Yajima
With our partners at Kasterstener Publications., Red Deer, AB, we have created an object oriented Model of the Human Anatomy. The model currently consists of over 3000 objects.
Funded by Genome Canada, we are now working to equip this model with functionality for the study of developmental patterns and diseases. More details can be found at the 4D Bioinformatics Web site. The most-asked question is what the "4" in 4D Bioinformatics stands for. This is of course the temporal component of our models. Have a look at the 4D demos (Flash Player required).
Principal Investigator: Christoph W. Sensen
Co-Investigators (from left to right): David Wishart (University of Alberta), Brian Fristensky (University of Manitoba), Mark Wilkinson (PBI, Saskatoon),
On April 2nd 2002, Genome Canada funded the Bioinformatics platform project to a total amount of 10 million dollars (5 million dollars from Genome Canada, to be matched by 5 million dollars of industrial and provincial contributions) over three years. The Bioinformatics platform builds on existing infrastructure at the Calgary-based Sun Center of Excellence for Visual Genomics.
The Platform was renewed in 2005 through an additional investement of approximately 5 Million Dollars by Genome Canada and is currently funded to the end of 2008.
The main scientific research
goals of the project focus on data standardization and Web Services (BioMOBY) and the
visualization of complex genomic features (Bluejay). A help desk and custom
programming facility assist genomics research projects in Canada on a
cost-recovery basis.
The project features a training component. Two Bioinformatics
workshops (approximately 50 students each) are held per year (one in Eastern and
one in Western Canada). These workshops are aimed at researchers working in Genome Canada science
projects or similar ventures. The goal is to create Bioinformatics “power users” who can
efficiently deal with the analysis and organization of the massive amounts of
data that will be produced in the currently more than 50 Genome Canada projects.
More details are available at the Project Web site.
Together with Terry Gaasterland (now at Scripps) I started the MAGPIE project in April 1995. MAGPIE is an automated genome analysis and annotation system. A major aspect of the project is the visualization of genomic features.
Below is one example of a view into a segment of the Sulfolobus solfataricus P2 genome.
Today, there are two versions of MAGPIE, a U.S. version based in Terry's laboratory and a Canadian version, based at the University of Calgary. Currently, Paul Gordon, Chris Koster and myself are working on the annotation of all publicly available genomes. The MAGPIE web site provides links to the annotated genomes.
Many questions that biologist would like to answer using completely sequenced genomes are complex. The ideal environment for questions like "Tell me where all the tRNA synthetase genes are and if they are co-located with the respective tRNA genes is a graphical environment. Over several years, we have created one of the most powerful browsers for XML-encoded genomic information. The system can be used free of charge by anyone. The Bluejay web site provides more details.
Bluejay Browser in Comparative Genomics Mode
I was part of the multinational Sulfolobus solfataricus P2 genome project, which concluded in 2001 with the publication of the entire genome.
We are now studying the gene expression of Sulfolobus in collaboration with several international collaborators.
The tools that we have developed for the Sulfolobus project, such as Magpie, Bluejay and Osprey, are now in wide use worldwide.
Together with scientists from the Canadian Food Inspection Agency in Lethbridge and Chronix Biomedical, Inc. in Göttingen, Germany, we have completed a study on the identification of DNA-based markers for transmissible spongiform encephalitis in Elk. We are now working with the Friedrich Löffler Institute in Riems, Chronix Biomedical, Inc and the University of Göttingen on a study of BSE-infected cattle.
Back to Christoph Sensen's home page
22.02.2011 |
