February 19, 2007
In many biological disciplines, and particularly in the field of genetics, the answers to scientists' questions are buried under mountains of complex data. In genome sequencing -- ordering the billions of chemical building blocks that make up the genetic code of a cell -- a newly discovered genome is compared to vast databases of well-known and publicly available genomes.
Comparing new genomes to these huge, and still growing, databases has become a task that is larger than one computer, even a supercomputer, can handle. Grid computing has stepped up to meet the challenge, with the help of the Genome Analysis Database Update tool.
GADU, which creates workflows, runs them on the Open Science Grid and TeraGrid, and stores the output, is a backend for applications used by geneticists for tasks ranging from biomedical applications to environmental cleanup. GADU runs on an average of 650-700 CPUs at a time, using more than 30 sites on the Open Science Grid and five clusters on the TeraGrid -- one of the few applications employing both grids simultaneously.
"The parallelization of data, running different tools as resource independent workflows, allows many sites from multiple grids to send jobs all at once," says Dinanath Sulakhe from the Computational Biology group at Argonne National Laboratory, who developed GADU with colleague Alex Rodriguez. "This saves on time, expense and human resources."
Margie Romine, a microbiologist at the Pacific Northwest National Laboratory in Richland, Washington, has used GADU to help her study the genetic code of the bacterium Shewanella oneidensis MR-1, whose metal- and radionuclide-reducing capability can impact the movement of such materials in the environment.
By using an application called GNARE that uses GADU, she is able to use genome sequences to better predict functions of proteins and map them to metabolic pathways that describe how proteins work together to synthesize and degrade cellular materials. By using this system to also study and compare MR-1 to other Shewanella genome sequences (18 in all), she hopes to gain a more comprehensive understanding of the diversity of Shewanella behavior in the environment.
"If you have a gateway to the grid like GADU, you can spend your time answering biological questions rather than worrying how to maintain and support your own computing facility," says Natalia Maltsev, head of Argonne's Computational Biology group. "Collaborators using this resource really depend on GADU, and we want to open it up to an even wider community."
Source: Open Science Grid
Jun 19, 2013 |
Ruan Pethiyagoda, Cameron Boehmer, John S. Dvorak, and Tim Sze, trained at San Francisco’s Hack Reactor, an institute designed for intense fast paced learning of programming, put together a program based on the N-Queens algorithm designed by the University of Cambridge’s Martin Richards, and modified it to run in parallel across multiple machines.
Jun 17, 2013 |
With that in mind, Datapipe hopes to establish themselves as a green-savvy HPC cloud provider with their recently announced Stratosphere platform. Datapipe markets Stratosphere as a green HPC cloud service and in doing so partnering with Verne Global and their Icelandic datacenter, which is known for its propensity in green computing.
Jun 12, 2013 |
Cloud computing is gaining ground in utilization by mid-sized institutions who are looking to expand their experimental high performance computing resources. As such, IBM released what they call Redbooks, in part to assist institutions’ movement of high performance computing applications to the cloud.
Jun 06, 2013 |
The San Diego Supercomputer Center launched a public cloud system for universities in the area designed specifically to run on commodity hardware with high performance solid-state drives. The center, which currently holds 5.5 PB of raw storage, is open to educational and research users in the University of California.
05/10/2013 | Cleversafe, Cray, DDN, NetApp, & Panasas | From Wall Street to Hollywood, drug discovery to homeland security, companies and organizations of all sizes and stripes are coming face to face with the challenges – and opportunities – afforded by Big Data. Before anyone can utilize these extraordinary data repositories, however, they must first harness and manage their data stores, and do so utilizing technologies that underscore affordability, security, and scalability.
04/02/2012 | AMD | Developers today are just beginning to explore the potential of heterogeneous computing, but the potential for this new paradigm is huge. This brief article reviews how the technology might impact a range of application development areas, including client experiences and cloud-based data management. As platforms like OpenCL continue to evolve, the benefits of heterogeneous computing will become even more accessible. Use this quick article to jump-start your own thinking on heterogeneous computing.