US: Associate Professor Daniel Janies, Ph.D., an expert in computational genomics at the Wexner Medical Center at The Ohio State University (OSU), and his colleagues had developed SUPRAMAP (supramap.org), a web-based application that synthesizes large, in 2007 to track the spread and evolution of pandemic (H1N1) and avian influenza (H5N1). Now, they developed a new client software application, GEOGENES (www.geogenes.org), to expand the capabilities of SUPRAMAP.
Prof Janies is working with software engineers at the Ohio Supercomputer Center (OSC) to expand the reach of SUPRAMAP so that researchers can better understand the spread of infectious diseases across hosts and geography. By separating SUPRAMAP’s client application from the underlying server software, the goal is to reconfigure the server in a way that researchers and public safety officials can develop other front-end applications that draw on the logic and computing resources of SUPRAMAP.
“Using SUPRAMAP, we initially developed maps that illustrated the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and in coronaviruses, such as SARS,” said Prof Janies. “SUPRAMAP allows the user to track strains carrying key mutations in a geospatial browser such as Google Earth. Our software allows public health scientists to update and view maps on the evolution and spread of pathogens.”
The original implementation of SUPRAMAP was built with a single client that was tightly coupled to the server software. “We now have decoupled the server from the original client to provide a modular web service for POY, (poyws.org) an open-source, freely available phylogenetic analysis programme developed at the American Museum of Natural History (AMNH). The web service can be used by other researchers with new ideas, data, and clients to create novel applications,” said Ward Wheeler, curator-in-charge of scientific computing at AMNH and a co-author with Janies and others on a recent article about the project in the journal Cladistics.
“To demonstrate the POY web service, we have produced a new client software application, GEOGENES (www.geogenes.org),” said Wheeler. “Unlike in SUPRAMAP, in which the user is required to create and upload data files, in GEOGENES the user works from a graphical interface to query a curated dataset, thus freeing the user from managing files.”
Currently this service is hosted on large shared systems at OSC, the center’s flagship HP Intel Xeon Oakley Cluster, their IBM Opteron Glenn Cluster and on a smaller dedicated cluster at Ohio State’s Wexner Medical Center.