Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Researchers take virus-tracking software worldwide

23.05.2012
Project allows new forms of client software to join genetic surveillance

A biomedical informatics researcher who tracks dangerous viruses as they spread around the globe has restructured his innovative tracking software to promote even wider use of the program around the world.

Associate Professor Daniel Janies, Ph.D., an expert in computational genomics at the Wexner Medical Center at The Ohio State University (OSU), is working with software engineers at the Ohio Supercomputer Center (OSC) to expand the reach of SUPRAMAP (supramap.org), a web-based application that synthesizes large, diverse datasets 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.

Janies and his colleagues at Ohio State, the American Museum of Natural History (AMNH) and OSC developed SUPRAMAP in 2007 to track the spread and evolution of pandemic (H1N1) and avian influenza (H5N1).

“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 Janies. “SUPRAMAP allows the user to track strains carrying key mutations in a geospatial browser such as Google EarthTM. 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 program developed at AMNH. The web service can be used by other researchers with new ideas, data, and clients to create novel applications,” said Ward Wheeler, Ph.D., curator-in-charge of scientific computing at AMNH and a coauthor 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.

“Decoupling the client from the server provides another advantage in that the implementation of the server can change to take advantage of advances in computing technology,” noted Thomas Bitterman, a senior software engineer at OSC and co-author of the journal article. “For example, the recent addition of the Oakley Cluster at OSC has made available a large set of GPUs that could result in performance improvements.”

To give their new software implementation a proper road test, the researchers examined groups of key mutations in a pathogen they hadn’t tracked before – the H7 avian influenza virus. Infection of humans by the H7 virus is rare, but it has occurred among people who have direct contact with infected poultry.

“H7 influenza, like H5N1 is largely an avian virus, but infects humans periodically, and therefore we wanted to see how it evolves,” said Janies. “We have shown that pathogenicity of the H7 influenza is highly labile on a molecular evolutionary level and has occurred independently in many places around the world. Now that the H5N1 papers detailing transmission among mammals have been published, we can next pinpoint the natural geographic distribution of key sets of mutations that could lead to human-to-human transmission. Our maps will allow scientists to better deploy public health resources to protect citizens and forces in the field.”

Grant funding through the U.S. Army Research Laboratory and Office supports this Innovation Group on Global Infectious Disease Research (gidr.osu.edu) project. Support for the computational requirements of the project comes from AMNH and OSC. Ohio State’s Wexner Medical Center, Department of Biomedical Informatics and offices of Academic Affairs and Research provide additional support.

____________
The Ohio Supercomputer Center (OSC), a member of the Ohio Technology Consortium of the Ohio Board of Regents, addresses the rising computational demands of academic and industrial research communities by providing a robust shared infrastructure and proven expertise in advanced modeling, simulation and analysis. OSC empowers scientists with the vital resources essential to make extraordinary discoveries and innovations, partners with businesses and industry to leverage computational science as a competitive force in the global knowledge economy, and leads efforts to equip the workforce with the key technology skills required to secure 21st century jobs. For more, visit www.osc.edu.

The Department of Biomedical Informatics at the Wexner Medical Center at The Ohio State University is a cross-disciplinary department, focusing on scientific data integration, imaging and simulation, medical informatics, computational biology and bioinformatics. The BMI staff leads the advancement of health and biomedicine through the development, application and dissemination of novel biomedical informatics theories and methods capable of driving biological discovery, generating and translating knowledge and advancing personalized healthcare. For more, visit biomed.osu.edu/bmi.

The American Museum of Natural History, founded in 1869, is one of the world’s preeminent scientific, educational, and cultural institutions. The Museum encompasses 45 permanent exhibition halls, including the Rose Center for Earth and Space and the Hayden Planetarium, as well as galleries for temporary exhibitions. Five active research divisions and three cross-disciplinary centers support 200 scientists, whose work draws on a world-class permanent collection of more than 32 million specimens and artifacts, including specialized collections for frozen tissue and genomic and astrophysical data, as well as one of the largest natural history libraries in the Western Hemisphere.. The Science Computer Cluster Facility is a major resource used by museum research scientists, postdoctoral fellows, and graduate and undergraduate students for high-end capability computing in the areas of biology, genomics, astrophysics, paleontology and anthropology. For more, visit research.amnh.org/scicomp/.

Mr. Jamie Abel | EurekAlert!
Further information:
http://www.osc.edu

More articles from Information Technology:

nachricht New technology enables 5-D imaging in live animals, humans
16.01.2017 | University of Southern California

nachricht Fraunhofer FIT announces CloudTeams collaborative software development platform – join it for free
10.01.2017 | Fraunhofer-Institut für Angewandte Informationstechnik FIT

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Interfacial Superconductivity: Magnetic and superconducting order revealed simultaneously

Researchers from the University of Hamburg in Germany, in collaboration with colleagues from the University of Aarhus in Denmark, have synthesized a new superconducting material by growing a few layers of an antiferromagnetic transition-metal chalcogenide on a bismuth-based topological insulator, both being non-superconducting materials.

While superconductivity and magnetism are generally believed to be mutually exclusive, surprisingly, in this new material, superconducting correlations...

Im Focus: Studying fundamental particles in materials

Laser-driving of semimetals allows creating novel quasiparticle states within condensed matter systems and switching between different states on ultrafast time scales

Studying properties of fundamental particles in condensed matter systems is a promising approach to quantum field theory. Quasiparticles offer the opportunity...

Im Focus: Designing Architecture with Solar Building Envelopes

Among the general public, solar thermal energy is currently associated with dark blue, rectangular collectors on building roofs. Technologies are needed for aesthetically high quality architecture which offer the architect more room for manoeuvre when it comes to low- and plus-energy buildings. With the “ArKol” project, researchers at Fraunhofer ISE together with partners are currently developing two façade collectors for solar thermal energy generation, which permit a high degree of design flexibility: a strip collector for opaque façade sections and a solar thermal blind for transparent sections. The current state of the two developments will be presented at the BAU 2017 trade fair.

As part of the “ArKol – development of architecturally highly integrated façade collectors with heat pipes” project, Fraunhofer ISE together with its partners...

Im Focus: How to inflate a hardened concrete shell with a weight of 80 t

At TU Wien, an alternative for resource intensive formwork for the construction of concrete domes was developed. It is now used in a test dome for the Austrian Federal Railways Infrastructure (ÖBB Infrastruktur).

Concrete shells are efficient structures, but not very resource efficient. The formwork for the construction of concrete domes alone requires a high amount of...

Im Focus: Bacterial Pac Man molecule snaps at sugar

Many pathogens use certain sugar compounds from their host to help conceal themselves against the immune system. Scientists at the University of Bonn have now, in cooperation with researchers at the University of York in the United Kingdom, analyzed the dynamics of a bacterial molecule that is involved in this process. They demonstrate that the protein grabs onto the sugar molecule with a Pac Man-like chewing motion and holds it until it can be used. Their results could help design therapeutics that could make the protein poorer at grabbing and holding and hence compromise the pathogen in the host. The study has now been published in “Biophysical Journal”.

The cells of the mouth, nose and intestinal mucosa produce large quantities of a chemical called sialic acid. Many bacteria possess a special transport system...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

12V, 48V, high-voltage – trends in E/E automotive architecture

10.01.2017 | Event News

2nd Conference on Non-Textual Information on 10 and 11 May 2017 in Hannover

09.01.2017 | Event News

Nothing will happen without batteries making it happen!

05.01.2017 | Event News

 
Latest News

Water - as the underlying driver of the Earth’s carbon cycle

17.01.2017 | Earth Sciences

Interfacial Superconductivity: Magnetic and superconducting order revealed simultaneously

17.01.2017 | Materials Sciences

Smart homes will “LISTEN” to your voice

17.01.2017 | Architecture and Construction

VideoLinks
B2B-VideoLinks
More VideoLinks >>>