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Primeur weekly 2015-10-26

Special

DZ Bank believes in Cloud computing but has to move with caution ...

Peter Coveney's views on the Virtual Human, the Human Brain Project, the medical practice and curriculum, and the interrelation of supercomputing and data storage ...

Focus

Exascale: not simply a matter of re-writing the applications and more parallelism ...

Exascale supercomputing

New report on energy-efficient computing ...

Photons open the gateway for quantum networks ...

Quantum computing

Loophole-free Bell test TU Delft crowns 80-years-old debate on nature of reality: Einsteins "spooky action" is real ...

Focus on Europe

IBM, UK STFC Hartree Centre, NVIDIA and Mellanox launch high performance computing POWER Acceleration and Design Center for business ...

Middleware

Bright Computing's Panos Labropoulos to speak at Amsterdam Spark Summit ...

Rogue Wave Software acquires enterprise PHP expert Zend ...

SGI exceeds 200 Terabyte milestone in total systems running SAP HANA ...

Hardware

Nor-Tech innovates ruggedized portable custom supercomputer for CAE and other applications ...

Comet: A supercomputer for the 'long tail' of science ...

U.S. Army unveils Excalibur, one of the world's top 20 supercomputers ...

Supermicro's new X11 UP solutions with highest performance and efficiency support latest Intel Xeon processor E3-1200 v5 family ...

New custom-designed storage system by DDN boosts Intel Omni-Path fabric speed in HPC, web and Cloud workflows by 100 percent ...

Department of Energy’s National Nuclear Security Administration selects Penguin Computing's Tundra extreme scale solution for National Labs ...

Applications

IBM expands data discovery and Q&A power of Watson Analytics ...

Cray's high-density GPU system sets new performance standard for ECHELON reservoir simulation software ...

New SDSC award provides easy path to supercomputing for neuroscientists ...

UC San Diego/SDSC study uncovers mechanism to block a cancer pathway ...

Utah researchers develop software to better understand brain's network of neurons ...

DrugDiscovery@TACC portal helps researchers worldwide with drug therapeutics ...

Supercomputing helps ecologists overturn popular theory ...

The Cloud

EMC and VMware reveal new Cloud services business ...

Dell introduces industry-first hybrid Cloud system with bold payment structure to simplify and minimize risks of Cloud adoption ...

DrugDiscovery@TACC portal helps researchers worldwide with drug therapeutics

21 Oct 2015 Austin - Where do you turn if you are a researcher who needs to quickly identify drug candidates for diseases ranging from obesity to tuberculosis to leishmaniasis, a tropical disease caused by the bite of a sand fly? You turn to the DrugDiscovery@TACC portal, which is currently helping more than 100 researchers worldwide model, simulate and generate data that is laying the foundation for new medicines. Thus far, more than seven million hours of computational work has been completed and dozens of drug leads have been found.

"Expanding our current portal into a freely-available, full-service centre for drug discovery and optimization would be even more valuable than what currently exists", stated Stan Watowich, one of the portal originators and associate professor in the Department of Biochemistry & Molecular Biology at The University of Texas Medical Branch in Galveston.

The Watowich Laboratory and the Texas Advanced Computing Center (TACC) at the University of Texas at Austin have been collaborating on the portal since 2013. Steve Mock, a portal developer, and John Fonner, a life sciences researcher worked directly with Watowich and his team to redevelop the portal. They did this on top of TACC's Agave Science-as-a-Service (SCaaS) platform to be more user friendly and to take advantage of the Lonestar 4 high performance supercomputer.

"With TACC's help, the user experience instantly became more robust, easier to negotiate, and much quicker to get your job submitted and completed", Stan Watowich stated.

Making a new therapeutic drug available to those who need it is a long process that ends with extensive clinical trials, according to Fonner. Getting to clinical trials, however, is dependent on finding and optimizing an effective drug candidate that binds strongly to the relevant biological target.

"The drug discovery portal lets researchers start with the biological target that is important to them and computationally test out hundreds of thousands of potential drug candidates using the physics of molecular interactions to find the best ones. From there, it is up to the researcher to pick which candidates to further optimize and test experimentally", he stated.

John Fonner continued: "By increasing the visual and analytics capabilities of the site, researchers will be able to explore their results through an interactive platform that can very quickly convey important binding information, allowing them to make decisions on which promising compounds to study further."

User data will move to Lonestar 5 in late 2015 and researchers will experience more power, speed, and overall capability. With 50 percent more cores than Lonestar4 and about four times the performance, users will get their drug discovery calculations done that much quicker. The new Cray XC40 supercomputer, which contains more than 30,000 Intel Xeon processing cores from the E5-2600 v3 product family, will provide a peak performance of 1.25 petaflops, and TACC expects the system to be in high demand.

"It's immensely satisfying to be a part of developing a tool that puts the complexity of the drug screening workflow and the power of TACC's supercomputers into the hands of researchers looking to help combat disease", Steve Mock stated. "This simple web interface democratizes access to a drug discovery pipeline previously unavailable to most people."

In terms of overall impact on research, this next level of supercomputing power will offer larger libraries for users to screen, and provide them with a larger chemical space to find possible drug candidates - "it's where the next level in the science will go", Stan Watowich stated.

The DrugDiscovery@TACC portal is not limited by geographic boundaries. In the Unites States and Europe, the portal provides researchers access to supercomputer resources to help them launch a drug discovery project with little effort - a point and click model. Researchers don't have to become a computational chemists themselves. They can take their disease target of interest and overnight obtain possible drug candidates, bring the computer predictions into the lab and test them doing the predictive work quickly.

The DrugDiscovery portal is also beneficial to researchers in developing countries that do not have access to high performance computing. All they need is a web browser and they can perform the same sophisticated calculations with the same supercomputer power that anyone in the developed world has at their fingertips. "In many cases, they would have large difficulties even conceiving doing this work", Stan Watowich stated. "We have researchers from a number of countries including Colombia, Cuba, Venezuela, and several countries in Africa. The portal has allowed them to start competing with research in the developed world."

After attending a workshop taught by Stan Watowich in 2014 in Medellin, Colombia, Carolina Quintero Gil of the Universidad Nacional received access to the portal. She stated: "Being able to participate in the course and having access to the portal helped me advance my research. I found commercial candidates to potently inhibit the Hepatitis E virus infection, a viral model of great importance in Colombia. Access to TACC resources saved me a lot of time and soon I will be able to start the in vitro evaluation of compounds found through the portal docking tool."

Stan Watowich, Steve Mock and John Fonner have many goals for the portal. One is to interface with IBM's World Community Grid (WCG), which has two million individual computers available for simulations and will add software to do more advanced molecular dynamic calculations to give more accurate predictions.

In addition, the team foresees developing and implementing software for generating new libraries and making visualizations available for researchers to download.

Finally, there's an additional component to integrate synthetic chemists into the mix. Once a researcher has a drug lead that works in the lab and in an animal model, it is important to bring it to the ‘high value' compound state, which means it is now a candidate for commercialization. "This is another component of the centre, which would be non-computational, but would leverage the computational prediction", Stan Watowich stated.

Portal user Jay Groppe, associate professor at the Texas A&M University Baylor College of Dentistry, summed up the value of the DrugDiscovery@TACC portal: "Without any previous experience in drug development, the way forward was unclear. An in silico screen could be conducted either commercially for tens of thousands of dollars, or after purchase of a software license and investment of significant time and effort learning routines of a suite of docking programmes."

Jay Groppe continued: "Through a tremendously opportune stroke of luck, the portal at TACC came to my attention and within days I was analyzing a long list of tantalizing dockings from the large 642,000+ drug-like compound library that eventually lead to the identification of novel allosteric inhibitors. As a result, a provisional patent has been filed, a seed-grant awarded and a solid NIH R01 proposal submitted. All without any experience or expense, yet with ready and willing support from TACC and UTMB. This is a remarkable resource and more scientists will realize this readily available asset at their disposal. I have enjoyed what is essentially a personal supercomputer for drug screening that rivals and likely surpasses any accessible to the large pharmaceutical concerns."
Source: University of Texas at Austin - Texas Advanced Computing Center - TACC

Back to Table of contents

Primeur weekly 2015-10-26

Special

DZ Bank believes in Cloud computing but has to move with caution ...

Peter Coveney's views on the Virtual Human, the Human Brain Project, the medical practice and curriculum, and the interrelation of supercomputing and data storage ...

Focus

Exascale: not simply a matter of re-writing the applications and more parallelism ...

Exascale supercomputing

New report on energy-efficient computing ...

Photons open the gateway for quantum networks ...

Quantum computing

Loophole-free Bell test TU Delft crowns 80-years-old debate on nature of reality: Einsteins "spooky action" is real ...

Focus on Europe

IBM, UK STFC Hartree Centre, NVIDIA and Mellanox launch high performance computing POWER Acceleration and Design Center for business ...

Middleware

Bright Computing's Panos Labropoulos to speak at Amsterdam Spark Summit ...

Rogue Wave Software acquires enterprise PHP expert Zend ...

SGI exceeds 200 Terabyte milestone in total systems running SAP HANA ...

Hardware

Nor-Tech innovates ruggedized portable custom supercomputer for CAE and other applications ...

Comet: A supercomputer for the 'long tail' of science ...

U.S. Army unveils Excalibur, one of the world's top 20 supercomputers ...

Supermicro's new X11 UP solutions with highest performance and efficiency support latest Intel Xeon processor E3-1200 v5 family ...

New custom-designed storage system by DDN boosts Intel Omni-Path fabric speed in HPC, web and Cloud workflows by 100 percent ...

Department of Energy’s National Nuclear Security Administration selects Penguin Computing's Tundra extreme scale solution for National Labs ...

Applications

IBM expands data discovery and Q&A power of Watson Analytics ...

Cray's high-density GPU system sets new performance standard for ECHELON reservoir simulation software ...

New SDSC award provides easy path to supercomputing for neuroscientists ...

UC San Diego/SDSC study uncovers mechanism to block a cancer pathway ...

Utah researchers develop software to better understand brain's network of neurons ...

DrugDiscovery@TACC portal helps researchers worldwide with drug therapeutics ...

Supercomputing helps ecologists overturn popular theory ...

The Cloud

EMC and VMware reveal new Cloud services business ...

Dell introduces industry-first hybrid Cloud system with bold payment structure to simplify and minimize risks of Cloud adoption ...