It’s all in the numbers

The key to infectious diseases could be in the numbers, and York now has the computing capacity to model how West Nile virus, SARS and perhaps – one day in the future – the bird flu, mutate and spread.

On Sept. 19, York celebrated the opening of a new parallel computing laboratory and the facility could provide essential information critical to combating the spread of disease. Known as the Laboratory of Mathematical Parallel Systems (LAMPS), the facility is the brainchild of a trio of York University researchers. Professors Huaiping Zhu (project leader), Steven Wang and Zijiang Yang received $250,045 from the Canada Foundation for Innovation (CFI) and a matching grant from the Ontario Innovation Trust (OIT) to set up a high-power parallel computing lab in the Department of Mathematics and Statistics at York University. The lab consists of a main server of 64 paralleled nodes and 18 workstations.

Right: Marking the official opening of York’s LAMPS facility are Professor Huaiping Zhu (left); Suzanne Corbeil, vice-president external relations, CFI; Stan Shapson, York’s vice-president, research & innovation; and David Bogart, executive director & chief operations officer, OIT

LAMPS is unique because it is a critical agent for researching the transmission of mosquito-borne diseases, such as the West Nile virus and infectious diseases, such as SARS. It will also enable researchers to work on classification of genes related to human diseases such as cancer; it provides a critical tool in drug discovery; and findings developed in LAMPS will be used to chart public health policy. The super computing capability built into the facilty provides researchers with the tools to compute the complex dynamics and manipulate large data sets. When dealing with bacterial or viral infections the numbers are in the trillions. That information combined with a host of other data sets including exponential growth of disease factors, carrier information, climatic data, drug treatment and vector control data provides a huge wealth of information which, in the past, could not always be effectively used.  

“This facility allows researchers to manipulate extremely large scale data sets with powerful computers,” said Stan Shapson, York’s vice-president, research & innovation. “It offers the kind of interdisciplinary research potential that York is known for.”

Left: Professor Huaiping Zhu (left); Robert Drummond, dean, Faculty of Arts; Gillian Wu, dean, Faculty of Science & Engineering; Steven Wang, LAMPS researcher; Zijiang Yang, LAMPS researcher; and, Neal Madras,  Chair, Department of Mathematics & Statistics

Suzanne Corbeil, vice-president external relations, CFI, agreed. “With the inauguration of LAMPS, we see tangible proof of the exciting research happening in Canada,” she said. “This lab will provide graduate students and postdoctoral fellows from a number of Faculties with access to leading edge research capability.”

According to Zhu, about 96 per cent of data goes unused because of the computing capacity required to manipulate and model the data. With the development of LAMPS, researchers now have the computer heft to work with this unused data. Clues to the spread of disease may be contained within that data and this opens up a new realm in research capability. The results of the research have future uses in project management, public health surveillance and policy management.

“The Faculty of Arts and the Department of Mathematics and Statistics have been very supportive in finding space for the lab and renovating the space,” said Zhu. “We have received wonderful support from the Office of the Vice-President, Research & Innovation, Office of Research Services, the Faculty of Science & Engineering, the Faculty of Arts and from Facilities York and the contractors who built the lab. Neal Madras, Chair, Department of Mathematics & Statistics, Gillian Wu, dean of the Faculty of Science & Engineering, and Robert Drummond, dean of the Faculty of Arts, have been very supportive and Generation 5 Mathematical Technologies and IBM have provided the software and hardware for the lab.”

Zhu’s work includes mathematical modelling and analysis in ecology and epidemiology as he studies transmission of mosquito-borne and infectious diseases. By using both analytical techniques for complex dynamic models and large scale simulations, Zhu can predict the possible outbreaks of the disease and its transmission pattern and make recommendations for public health policy.

Wang is building sophisticated statistical models for classifications and predictions. These models will be applied to find lead compounds for drug discovery and to understand protein functions. He and his research team members will also develop advanced statistical algorithms to partition massive data sets into smaller and more interpretable subsets. The findings will have wide applications to data mining.

Yang’s research is focused on information technology (IT) investment evaluation, performance analysis and data mining algorithms.  Her research on evaluating IT investment will provide an objective tool to measure IT performance and provide a science-based guideline for companies to optimize IT spending. Performance analysis, meanwhile, can have a significant impact on improving managerial performance. In addition, the findings will provide a peer group for comparisons. This information can be applied in many fields, from banking to bioinformatics.

Visit the LAMPS Web site for more information on the project or call ext. 55250. The facility is located in N532 Ross Bldg., on York’s Keele campus.