Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Europe's DEISA and GridAustralia demonstrating interoperation with distributed supercomputing for HIV drug simulations

14.12.2007
DEISA, the Distributed European Infrastructure for Supercomputing Applications, and GridAustralia-APAC, joined by Monash University, have demonstrated interoperation of their HPC infrastructures with distributed simulations in both continents on the effectiveness of drugs on mutants of the Human Immunodeficiency Virus HIV.

The AIDS disease effects over 40 million people worldwide. Certain drugs have the ability to reduce patient viral loads and improve patient health by binding to and inhibiting critical viral enzymes. Unfortunately, the HIV virus causing AIDS has the ability to mutate and become resistant to these drugs. That sometimes happens in a very short period of time, thus requiring the patients to change their drug regime. As new mutations arise, it is important to pick the right anti-viral drug to best treat the patient and to not encourage the development of further drug resistance.

According to Michael Kuiper from VPAC, simulations have been designed to gather drug binding interaction energies of anti-HIV drugs bound to the active site of HIV protease, including drug-resistant versions of the protein. Though a metho¬dology with still ongoing development, it is hoped that this technique can give an accurate assessment of the likely effectiveness of each antiviral drug with respect to any given HIV mutant strain.

Given this information, patients who develop drug resistance can be given the next best effective drug for their HIV strain while reducing the danger of further resistance enhancements. In order to assess the drug binding interactions, each drug and respective HIV mutant enzyme is run as a short molecular dynamics simulation to try and get an averaged energy of interaction between the drug and the HIV protease strain. The huge number of calculations required is well suited for distributed processing, and time-to-solution can be significantly reduced by employing at the same time several supercomputers in a suitable HPC grid. Given a certain level of interoperability, the compute tasks can even be spread over different grids.

This effort has been successfully undertaken by DEISA and GridAustralia-APAC, joined by Monash University, during SC07 in Reno, although both infrastructures use different, incompatible underlying main middleware platforms.

DEISA is based on UNICORE 5 as far as job submission is concerned, while APAC makes use of the Globus Tool Kit. Following different approaches in job management, Globus and UNICORE are not interoperable in their currently established versions. In addition to DEISA’s option of data management via a continental global file system, however, both infrastructures support data transfer via GridFTP, usable both in Globus and in UNICORE.

Input data sets were provided in Australia by the Australian Research Group on an APAC storage server. Series of workflow jobs were submitted as shell scripts at the client site both to DEISA and to APAC through infrastructure specific interfaces, using DESHL for DEISA (a UNICORE command line tool), and Globus WS-Gram client for APAC. The parts of the input data required by each job were automatically moved to the respective DEISA or APAC execution sites in Europe or Australia via GridFTP.

A number of simulations were run with the drug Amprenavir (Apv) acting on various HIV strains. The trajectory data was post-processed to measure the energy of interaction between the drug and each HIV strain. The simulation results were later automatically uploaded on that APAC storage server for post-pro-cessing and visualization by the researchers.

By this transparent linking of compute resources in Australia and in Europe, and by offering reliable, automated bidirectional data transfer between both infrastructures, this project-oriented interoperation of DEISA and APAC could successfully be demonstrated for the first time.

Saara Vaerttoe | alfa
Further information:
http://www.deisa.org/

More articles from Information Technology:

nachricht UT professor develops algorithm to improve online mapping of disaster areas
29.11.2016 | University of Tennessee at Knoxville

nachricht New standard helps optical trackers follow moving objects precisely
23.11.2016 | National Institute of Standards and Technology (NIST)

All articles from Information Technology >>>

The most recent press releases about innovation >>>

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

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

Im Focus: Molecules change shape when wet

Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water

In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...

Im Focus: Fraunhofer ISE Develops Highly Compact, High Frequency DC/DC Converter for Aviation

The efficiency of power electronic systems is not solely dependent on electrical efficiency but also on weight, for example, in mobile systems. When the weight of relevant components and devices in airplanes, for instance, is reduced, fuel savings can be achieved and correspondingly greenhouse gas emissions decreased. New materials and components based on gallium nitride (GaN) can help to reduce weight and increase the efficiency. With these new materials, power electronic switches can be operated at higher switching frequency, resulting in higher power density and lower material costs.

Researchers at the Fraunhofer Institute for Solar Energy Systems ISE together with partners have investigated how these materials can be used to make power...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

UTSA study describes new minimally invasive device to treat cancer and other illnesses

02.12.2016 | Medical Engineering

Plasma-zapping process could yield trans fat-free soybean oil product

02.12.2016 | Agricultural and Forestry Science

What do Netflix, Google and planetary systems have in common?

02.12.2016 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>