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CIPRES Offers Gateway to Supercomputing Life Sciences

New tree of life. Researchers credit the CIPRES science gateway for easy access to XSEDE supercomputers as they added over 1000 bacteria and prokaryotes to the tree of life. Courtesy Laura Hug, Jill Banfield, and Nature Microbiology.

New tree of life. Researchers credit the CIPRES science gateway for easy access to XSEDE supercomputers as they added over 1000 bacteria and prokaryotes to the tree of life. Courtesy Laura Hug, Jill Banfield, and Nature Microbiology.

In this special guest feature, Lance Farrell from Science Node writes that CIPRES is a web-based gateway that allows researchers to easily explore evolutionary relationships between species using NSF supercomputers.

Infrastructure is one of those boring but essential components of civilization. Your commute, your morning shower, your quick glance online — these and many other steps in the modern world would be grueling, unthinkable endeavors were it not for the groundwork laid years ago by forward thinkers.

Visionaries like the US National Science Foundation (NSF) long ago perceived the value of infrastructure. Their investment enables the basic research that flows out and makes our society better.

One of their most audacious and prescient moves was to invest in the national high-performance computing (HPC) infrastructure, as seen in XSEDE (eXtreme Science and Engineering Discovery Environment), for instance.

More courageous still was the recognition that scientists with smaller projects could accelerate their work with a small allocation of time on these behemoth compute machines. Supercomputers, the NSF saw, were not only for the massive computing tasks, but could also benefit those in the so-called ‘long tail of science.’

I can’t say enough about how inspired and important that decision was,” says Mark Miller, principal investigator on the Cyberinfrastructure for Phylogenetic Research (CIPRES) project. “I know of no other governmental organization in the world that allows their big machines to be used in this way: For small jobs, and for everyone in the world.”

CIPRES

CIPRES offers access to HPC resources through a browser interface and a set of enabling public web interfaces. Think of it as a gateway that allows researchers to easily explore evolutionary relationships between species using NSF supercomputers.

The NSF seeds the discoveries that are a bridge to the future. ~ Mark Miller.

In the six years since it was established, CIPRES has enabled 2,300+ scientific publications, while only occupying about 1% of the NSF supercomputing resources. That’s an impressive return on investment.

Since its inception, CIPRES has had broad appeal, as it has served a diverse swath of user groups.

In the past year, CIPRES has submitted jobs for nearly 2,000 users from 330 institutions across the US and its territories. Of these institutions, four are historically black colleges, 24 are Hispanic-serving institutions, and two are Alaska and Hawaii native-serving institutions — four are high schools.

CIPRES usage:

  • 2,300 scientific publications
  • 6,500+ users
  • 85+ different countries
  • 22 US federal agencies

CIPRES has also been central to jobs run for 29 of the 31 regions participating in the NSF’s Experimental Program to Stimulate Competitive Research (EPSCoR). CIPRES has received submissions from 24 non-governmental agencies and related independent research institutes, 13 museums, 7 botanical gardens, two zoos, and four commercial entities in the US.

In addition, jobs were submitted for staff at 22 US federal and state government agencies, including NASA, NOAA, and the Departments of Health and Human Services, Defense, Interior, Energy, and Commerce.

Outside the US, CIPRES has served 4,500+ users in nearly 1,000 institutions in 85 different countries.

Science makers

With all the scientific publications it has aided, it is easy to see CIPRES’s imprint on scientific discovery. Most of its users rave about the time and resources conserved through the NSF investment.

For instance, the scientists behind the recently revised tree of life published in Nature Microbiology credit CIPRES for their breakthrough.

Prior to our introduction to CIPRES,” says lead author Laura Hug, “no run had successfully finished. The CIPRES science gateway was critical to our work.”

Hug’s team found their supercomputer resources through the CIPRES gateway. They began with Gordon at the San Diego Supercomputer Center, and created the final trees on Comet, both NSF XSEDE machines. In total, the two jobs ran for about five days, using 48 cores.

In another recent discovery made possible by CIPRES, researchers were able to map the horizontal gene transfer from nematodes to birds. Thanks to CIPRES, these scientists were able to propose deer flies as the vector point for the genetic transfer.

Flash Gordon. The SDSC supercomputer Gordon, with 300TB of flash-based storage, aided researchers who recently revised the tree of life. Access and use was a snap with the CIPRES science gateway.

Flash Gordon. The SDSC supercomputer Gordon, with 300TB of flash-based storage, aided researchers who recently revised the tree of life. Access and use was a snap with the CIPRES science gateway.

For young researchers at the transition of postdoc to PI,” says lead author Alexander Suh, “CIPRES is an important resource because we usually lack the funding and or infrastructure for these kind of analyses. CIPRES has helped me a lot towards achieving scientific independence.”

Suh’s refrain is heard over and again everyday across the US. Where lack of access to HPC resources would have foundered research in the past — because it was being done in the jungles of Panama, or simply at an HPC-poor university — NSF investment in infrastructure has made scientific advance possible.

“The NSF is an incredibly important engine for discovery in the US,” says Miller.

“They seed the discoveries of basic research, discoveries that are not just novel science — they are a bridge to the future where the US is competitive with other countries making large investments in research, where quality of life is improved, and where humanity is better equipped to create a sustainable planet for the next generation.”

XSEDE16 will be held in Miami from July 17-21. This year’s theme is Diversity, Big Data, & Science at Scale: Enabling the next generation of Science and Technology.

Source: Science Node under the Creative Commons License

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