What we do
Powering Cancer Research
Cancer Computer exists because there simply aren’t enough computing resources available to cancer researchers, and the demand for computing is increasing every year at greater rate than the resources being deployed for their use.
Moreover, this gap is widening.
HOW DOES A COMPUTER CURE CANCER?
While many may not see the connection, super computers play a large role in today’s research. Many researchers use the immense computing power of super computers to run complex experiments. Through mathematical modelling and computational simulations, researchers can better understand the biological processes that occur within a cell, translating the genetic information stored in our DNA into physical characteristics and traits that we can see.
“Computational biology has the potential to do this. It is a tool used to rigorously and mathematically describe and investigate biological processes, impacting our understanding of genetics and healthcare. Computational biology has the potential to become one of the most important areas of scientific research in the twenty-first century,” says Dr. Tatiana Tatarinova, University of South Wales, Genomics and Computational Biology Research Group.
While great progress has been made in the advancing research in the cure for cancer, there are hidden challenges researchers face.
Shortage of Available Super Computers
In February 2016, The Globe and Mail reported that scientists across Canada who need access to fast and powerful supercomputers to conduct their federally funded research say they are falling behind their international competitors, or having to switch to less ambitious projects because the country’s digital research infrastructure is insufficient to meet their needs.
What’s needed is not simply more data storage but also computational capacity – the ability to crunch through reams of calculations to do things like analyze genetic variants across an entire population.
Compute Canada, the organization tasked with supporting university-based researchers with their digital needs, says that the growing reliance on computation in many areas of science means that it is no longer able to provide its biggest users with the digital muscle they need to operate in the world’s top tier. The organization projects that more modest users of its services could be running into similar barriers in the next couple of years.
Cost to Access Super Computers
In addition to the shortage of access to super computers, scientists also have to face the cost to utilize these massive systems. Researchers spend much of their valuable time writing grant proposals, sourcing funding for their research, and dealing with administrative red tape.
Our goal is to ensure that researchers have subsidised, and in some cases free, access to the computing power they need. This will limit the amount of time needed to source funding and allow researchers more time to focus on their goals.
An improved understanding of the genetic factors underlying the onset of cancer in each individual patient will lead to the development of improved—and personalized—methods for that patient’s treatment.
Cancer Computer’s cloud-based platform allows for easy scalability at a fraction of the cost of today’s data centres.
More access means more research, which will result in better treatments and a quicker road to a cure.
How Cancer Computer Helps
Cancer Computer helps relieve the high cost and long wait times facing cancer researchers, offering a host of IT resources they need to further their research.
Infrastructure is the computers, storage devices, and networking, that make up our high performance computing (HPC), high throughput computing (HTC), “Big Data” analytics, machine learning, Cloud services, etc. We currently have 5 clusters of servers, located in secure collocation facilities, across North America, that provide the “computing power” to get cancer research work, such as structural biology, genomics, proteinomics, and other kinds of bioinformatics work done. In many cases, we simply provide free or heavily discounted cloud resources, to resources, much like a regular cloud provider, except for far less cost. Valuable for researchers or research hospitals on limited budgets.
Applications are the software tools that the researchers actually use. There are literally thousands of tools that can be used in many ways, including using many of them in “workflows” to complete work. This work can be done on Cancer Computer’s own infrastructure, or cloud, or in coordination with other research institutions. It depends on the nature of the work.
Creating some of the workflows, net-new applications, or even systems integration, can be very challenging work. For this, we have supercomputing and IT experts to assist researchers. We become their technical partners, and they can focus on their research. Many of those applications involve AI (machine learning, natural language processing, etc.) and the use of “Big Data” (very large data sets) that Cancer Computer can not only provide the infrastructure for, but can assist in improving outcomes for research, in both the areas of improving speed and reproducibility.
Some of the current projects and partners using the Cancer Computer platform:
Princess Margaret Cancer Center
(Mapping Cancer Markers)
University of Guelph, Institute for Comparative Cancer Investigation
(Cancer Computer Cloud)
Indiana University Medical School
(OSG – Splinter Project)
Harvard Medical School
(OSG – Structural Biology Grid)
University of Nebraska Medical Center
(OSG-XSEDE – Meta-genomics and Cancer research data)
University of California, San Francisco
(OSG-XSEDE – Custom protein design)
(OSG – Constructing gene interaction graphs at high scale)
University of Minneapolis and St. Paul – University Enterprise Labs
(Accelerating molecular dynamics with supervised AI)
(Folding @ Home, a public project, scavenged CPU+GPU cycles)
University of Washington
(Rosetta @ Home, a public project, scavenged CPU cycles)
Saga Medical Center Koseikan, Japan
(Smash Childhood Cancer, a public project, scavenged CPU cycles)
The Supercomputer for Cancer Research