Information Technology seminars

MURPA Seminar - Cyberinfrastructure for Avian Flu Drug Design: have the cake and eat it too

Date and time:

28/08/2008, 9:30

Location:

Building: 26, Room: 135, (via HD interactive wall) Clayton Campus

Presenters:

Dr. Wilfred Li Executive Director National Biomedical Computation Resource UCSD

Abstract:

Biomedical, translational and clinical research  through increasingly complex computational modeling and simulation  generate enormous potential for personalized medicine and therapy,  and an insatiable demand for advanced cyberinfrastructure (CI). New  programming models and workflow management tools are required to  allow researchers to move quickly from pilot studies to large-scale  simulation experiments. Massive datacenters, aka, cloud computing,  have emerged to offer very large petascale computing environment.  Effective middleware that help existing scientific applications to  gain integrated access to computation, data and visualization  resources are required. They must be highly reusable and yet  customizable based upon the specific needs of a particular scientific  community.

We have been working with both scientific researchers and  infrastructure developers to transform innovative multiscale modeling  and simulation tools to maximize their potential in large-scale  scientific inquiries. The Avian Flu Grid (AFG) project grew out of  the collaborative activities in the Biosciences and Resources working  groups of the Pacific Rim Applications and Middleware Assembly  (PRAMGA). The AFG virtual organization (VO) is dedicated to  collaborative research on antiviral drug discovery for potentially  pandemic influenza viruses. Currently, we have enabled the molecular  dynamics applications such as NAMD and virtual screening applications  such as AutoDock to be exposed as Opal based services. These services  may be invoked within the usual user environment such as ADT  (AutoDockTools) while the jobs are executed remotely on grid  resources such as the PRAGMA grid or the TeraGrid. Application  specific user interfaces may be specified and automatically generated  within various types of clients, including advanced workflow  management tools such as Vision and Kepler.

Students from the PRIME (Pacific RIM undergraduate Education)  project are currently using this environment in their summer  internship in the search for avian flu inhibitors. We report a set of  potentially novel inhibitors for H5N1 neuraminidase N1 that are  discovered in ensemble based virtual screening experiments using the  relaxed complex method. Moreover, comparative molecular dynamics  studies on different clades of hemagglutinin proteins (HA) have  yielded potentially novel mechanism of host tropism. These studies  present exciting opportunities to leverage the growing computing  power, and pose further challenges for efficient CI development.

Speaker biographies:

Wilfred W. Li received his Ph.D. in Biochemistry and Molecular  Biology from the University of Southern California (USC) in 1994  where he studied the molecular chaperone GRP78/BiP as a model system  for gene regulation and protein-DNA interactions. While a  postdoctoral fellow at the University of California, San Diego  (UCSD), he contributed to the understanding of protein phosphatases  in cell growth and apoptosis in the JNK/SAPK pathway. He became a  senior fellow in Bioinformatics at the San Diego Supercomputer  Center, UCSD, in 1999, and studied structure based proteome  annotation. He is currently the Executive Director of the National  Biomedical Computation Resource (NBCR at http://nbcr.net), UCSD,  adjunct lecturer at the School of Information Technology, Osaka  University, Japan, and adjunct professor at the College of Computer  Science and Technology, Jilin University, PRC. His current research  interests include cluster and grid computing, cyberinfrastructure,  high throughput proteome annotation, data mining, virtual screening,  structure based drug discovery, multiscale modeling and visualization.

For more information, visit:

http://www.sdsc.edu/~wilfred/

Enquiries:

Ronald Pose

Research group website:

http://www.infotech.monash.edu.au/about/events/2008/murpa.html