Gateways for Open Science

By Elizabeth Murray, National Center for Supercomputing Applications

August 12, 2013

“Science is really ripe for disruption. A lot of the practices are still very much rooted in their analog beginnings.” That is how Kaitlin Thaney, Director of the Mozilla Science Lab—a new open science initiative focused on innovation, best practice, and skills training for research—began her plenary talk at XSEDE13 in San Diego last month.

Thaney believes that the web has fundamentally transformed how we interrogate, how we interact with content, how we discover information, our work environments, and our agility. “We at Mozilla are focusing on how we can help researchers use the power of the open web to change science’s future,” she said.

The Mozilla Science Lab is funded by the Alfred P. Sloan Foundation, a leading funder in digital scholarship and information technology with projects focused on data sharing, new forms of metrics for scholarly research, and other technologies on the library side. Thaney sees this as a larger play to see how all of them can work together toward a broader means of coordinating these various efforts to provide infrastructure and also leadership in the open science space while pushing this practice into the mainstream.

Thaney makes the case that our current systems are still designed to create friction despite their original intentions. “Modern discoveries are still locked up in various silos and not as interlinked as they could be,” she said. “Even looking at the way we reward scientific contribution, it is still very much reliant on a paper-based system. We are starting to see what the behavioral effects will be from this sort of reward system, and what we are seeing is more error creep into the way research is done.”

Citing Elizabeth Iorns, Co-founder of Science Exchange, Thaney said that “up to 70 percent of research from academic labs cannot be reproduced, representing an enormous waste of money and effort.” She pointed to this statistic as reflective of a larger problem that the research community should address by developing a better way to reflect and reward research contributions and practices. “It is really keeping us from that whole notion of building on additional knowledge, or prior knowledge, or standing on the shoulders of giants, and really looking at how we can start to minimize not only the amount of error but also the amount of duplication,” said Thaney.

Moving Forward

Luckily we have the Internet, which Thaney views as one of the most important advances since the printing press; however, inventing and putting into practice are two very different things. “Even though the web was created by scientists, I think we can all probably largely agree that the web has not yet transformed science in the same way that it has transformed the way we do business or the way we look at education,” said Thaney.

Step one is gateways. It is no coincidence that there are commonalities between her project at Mozilla and XSEDE’s Science Gateways, the theme of XSEDE13. Both look at preparing web-based resources so science and engineering researchers can have better access to the data, the information, the software, and the code through online community spaces. Both hope making these tools more accessible will increase the power behind the computation.

Thaney said that in her previous work at the technology company Digital Science they were looking at application-based technologies that would help bring researchers a little bit closer to a world of reproducibility and better practice via the web. They found that the most successful work was with tools that were mapped into a ubiquitous layer, where users didn’t even realize they were interacting with a web-based tool anymore.

Closing the Gap

Starting with the physical aspects of research—the lab mice, the DNA, the cell lines—there are ways to attach digital imprints. “Whether it’s a tracking number or some other means of attaching identity to it, the community can start to integrate that into the systems to make it a little bit easier for the next researcher who comes along to be able to reproduce and start from that without having to reverse engineer,” explained Thaney.

Research isn’t cheap, she reminded the conference attendees. “For example, getting one Huntington’s protein, that can cost you $400, only to get it to your lab and realize there is a massive efficacy issue around using various proteins and antibodies. And now you need to start from scratch again.”

MozillaFondation1“The Mozilla Science Lab is looking at what we could possibly learn from the open source community, both in terms of culture and technology,” said Thaney. That community believes that sharing risk and also reward by mixing internal and also external involvement and development will often times get you much further toward your goal. “Looking at the broader idea of having innovation not just be putting your own ideas into a funnel and then pushing it out to the greater world, but having it be much more of a porous process,” Thaney said.

Thaney’s and Mozilla’s mission also includes increasing digital literacy. Relying on ad-hoc, self-taught practices to close the gap between what you are expected to know and what you have the resources to learn doesn’t scale, according to Thaney. “The amount of times researchers have come to me and said ‘I wanted to do this post-doc but my PI told me I need to know Python along with a range of things I have never experienced before, and so I just bought a book.’ That is not best practice.”

One way the Mozilla Science Lab is increasing digital literacy is by working with a program called Software Carpentry. The program teaches basic computational competency and digital skills to researchers to help provide the springboard needed for 21st century science.

Measuring Up and Fighting Fears

A traditional metric for evaluating the impact of scholarly research has been the number of times an article is cited; however, with the growing use of alternative metrics, or “altmetrics,” citation is no longer the only way to measure success. How many times an article has been bookmarked, tweeted, shared, blogged about, or cited in Wikipedia can now matter just as much. “The data there is actually quite staggering in some context. Where a paper it is associated with might be cited ten times, the data might be reused 1,500. That is really powerful to be able to go to your funder or be able to go to your research administrator and say this is a useful bit of my research,” explained Thaney.

Thaney understands the fear that goes along with the practice of open science: “Relinquishing information and opening it up for anyone to make use of it can be slightly terrifying, especially when there is a lot of time that goes into collecting that information, but using the power of the network, we can really have the opportunity to open it up to as many eyes as possible to see the broader use and impact of what that research may be.”

XSEDE13 participant Anthony Frachioni, who will enter into the physics PhD program at Binghamton University, New York, in the fall, said that while he is excited at the prospect of an open science and research world, at the end of the day he still lives in constant fear he will get scooped. “What do you do about credit and courtesy?” he asked Thaney.

“A lot of it comes down to being human. The technology there has shown we have the ability to start to making this information available, but when it comes to the reward mechanisms, we need to start providing some sort of assurance, because otherwise, we can only go so far,” she responded. “I can say that researchers getting scooped simply because they made some information available early happens a lot less than you might think, but I understand when it comes to job security, we need something far more concrete.”

Thaney said that concern is why Mozilla, through a separate program, is looking into ways to provide badges, or some other sort of accolade within the researcher’s university or institution, to show proof of intellectual property in a particular area. The hope is that having something to show for sharing information will provide comfort for the researcher while cautioning others to think twice about scooping it. “It is not an easy problem to solve, but we are working on it,” concluded Thaney.

Even without concrete solutions, Frachioni remains enthusiastic about the possibilities of open science. “This is all completely unprecedented, and that isn’t going to give us any reassurance at the end of the day,” he said, “but I think that it’s our responsibility to enter into this knowing that and knowing that we should do it anyway.”

The annual XSEDE conference, organized by the National Science Foundation’s Extreme Science and Engineering Discovery Environment with the support of corporate and non-profit sponsors, brings together the extended community of individuals interested in advancing research cyberinfrastructure and integrated digital services for the benefit of science and society. XSEDE13 was held July 22-25 in San Diego; XSEDE14 will be held July 13-18 in Atlanta. For more information, visit https://conferences.xsede.org/xsede14.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “pre-exascale” award), parsed out additional information ab Read more…

By Tiffany Trader

Tsinghua Crowned Eight-Time Student Cluster Champions at ISC

June 22, 2017

Always a hard-fought competition, the Student Cluster Competition awards were announced Wednesday, June 21, at the ISC High Performance Conference 2017. Amid whoops and hollers from the crowd, Thomas Sterling presented t Read more…

By Kim McMahon

GPUs, Power9, Figure Prominently in IBM’s Bet on Weather Forecasting

June 22, 2017

IBM jumped into the weather forecasting business roughly a year and a half ago by purchasing The Weather Company. This week at ISC 2017, Big Blue rolled out plans to push deeper into climate science and develop more gran Read more…

By John Russell

Intersect 360 at ISC: HPC Industry at $44B by 2021

June 22, 2017

The care, feeding and sustained growth of the HPC industry increasingly is in the hands of the commercial market sector – in particular, it’s the hyperscale companies and their embrace of AI and deep learning – tha Read more…

By Doug Black

HPE Extreme Performance Solutions

Creating a Roadmap for HPC Innovation at ISC 2017

In an era where technological advancements are driving innovation to every sector, and powering major economic and scientific breakthroughs, high performance computing (HPC) is crucial to tackle the challenges of today and tomorrow. Read more…

At ISC – Goh on Go: Humans Can’t Scale, the Data-Centric Learning Machine Can

June 22, 2017

I've seen the future this week at ISC, it’s on display in prototype or Powerpoint form, and it’s going to dumbfound you. The future is an AI neural network designed to emulate and compete with the human brain. In thi Read more…

By Doug Black

Cray Brings AI and HPC Together on Flagship Supers

June 20, 2017

Cray took one more step toward the convergence of big data and high performance computing (HPC) today when it announced that it’s adding a full suite of big data and artificial intelligence software to its top-of-the-l Read more…

By Alex Woodie

AMD Charges Back into the Datacenter and HPC Workflows with EPYC Processor

June 20, 2017

AMD is charging back into the enterprise datacenter and select HPC workflows with its new EPYC 7000 processor line, code-named Naples, announced today at a “global” launch event in Austin TX. In many ways it was a fu Read more…

By John Russell

Hyperion: Deep Learning, AI Helping Drive Healthy HPC Industry Growth

June 20, 2017

To be at the ISC conference in Frankfurt this week is to experience deep immersion in deep learning. Users want to learn about it, vendors want to talk about it, analysts and journalists want to report on it. Deep learni Read more…

By Doug Black

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

Tsinghua Crowned Eight-Time Student Cluster Champions at ISC

June 22, 2017

Always a hard-fought competition, the Student Cluster Competition awards were announced Wednesday, June 21, at the ISC High Performance Conference 2017. Amid wh Read more…

By Kim McMahon

GPUs, Power9, Figure Prominently in IBM’s Bet on Weather Forecasting

June 22, 2017

IBM jumped into the weather forecasting business roughly a year and a half ago by purchasing The Weather Company. This week at ISC 2017, Big Blue rolled out pla Read more…

By John Russell

Intersect 360 at ISC: HPC Industry at $44B by 2021

June 22, 2017

The care, feeding and sustained growth of the HPC industry increasingly is in the hands of the commercial market sector – in particular, it’s the hyperscale Read more…

By Doug Black

At ISC – Goh on Go: Humans Can’t Scale, the Data-Centric Learning Machine Can

June 22, 2017

I've seen the future this week at ISC, it’s on display in prototype or Powerpoint form, and it’s going to dumbfound you. The future is an AI neural network Read more…

By Doug Black

Cray Brings AI and HPC Together on Flagship Supers

June 20, 2017

Cray took one more step toward the convergence of big data and high performance computing (HPC) today when it announced that it’s adding a full suite of big d Read more…

By Alex Woodie

AMD Charges Back into the Datacenter and HPC Workflows with EPYC Processor

June 20, 2017

AMD is charging back into the enterprise datacenter and select HPC workflows with its new EPYC 7000 processor line, code-named Naples, announced today at a “g Read more…

By John Russell

Hyperion: Deep Learning, AI Helping Drive Healthy HPC Industry Growth

June 20, 2017

To be at the ISC conference in Frankfurt this week is to experience deep immersion in deep learning. Users want to learn about it, vendors want to talk about it Read more…

By Doug Black

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Just how close real-wo Read more…

By John Russell

Trump Budget Targets NIH, DOE, and EPA; No Mention of NSF

March 16, 2017

President Trump’s proposed U.S. fiscal 2018 budget issued today sharply cuts science spending while bolstering military spending as he promised during the cam Read more…

By John Russell

HPC Compiler Company PathScale Seeks Life Raft

March 23, 2017

HPCwire has learned that HPC compiler company PathScale has fallen on difficult times and is asking the community for help or actively seeking a buyer for its a Read more…

By Tiffany Trader

Google Pulls Back the Covers on Its First Machine Learning Chip

April 6, 2017

This week Google released a report detailing the design and performance characteristics of the Tensor Processing Unit (TPU), its custom ASIC for the inference Read more…

By Tiffany Trader

CPU-based Visualization Positions for Exascale Supercomputing

March 16, 2017

In this contributed perspective piece, Intel’s Jim Jeffers makes the case that CPU-based visualization is now widely adopted and as such is no longer a contrarian view, but is rather an exascale requirement. Read more…

By Jim Jeffers, Principal Engineer and Engineering Leader, Intel

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Nvidia’s Mammoth Volta GPU Aims High for AI, HPC

May 10, 2017

At Nvidia's GPU Technology Conference (GTC17) in San Jose, Calif., this morning, CEO Jensen Huang announced the company's much-anticipated Volta architecture a Read more…

By Tiffany Trader

Facebook Open Sources Caffe2; Nvidia, Intel Rush to Optimize

April 18, 2017

From its F8 developer conference in San Jose, Calif., today, Facebook announced Caffe2, a new open-source, cross-platform framework for deep learning. Caffe2 is the successor to Caffe, the deep learning framework developed by Berkeley AI Research and community contributors. Read more…

By Tiffany Trader

Leading Solution Providers

MIT Mathematician Spins Up 220,000-Core Google Compute Cluster

April 21, 2017

On Thursday, Google announced that MIT math professor and computational number theorist Andrew V. Sutherland had set a record for the largest Google Compute Engine (GCE) job. Sutherland ran the massive mathematics workload on 220,000 GCE cores using preemptible virtual machine instances. Read more…

By Tiffany Trader

Google Debuts TPU v2 and will Add to Google Cloud

May 25, 2017

Not long after stirring attention in the deep learning/AI community by revealing the details of its Tensor Processing Unit (TPU), Google last week announced the Read more…

By John Russell

US Supercomputing Leaders Tackle the China Question

March 15, 2017

Joint DOE-NSA report responds to the increased global pressures impacting the competitiveness of U.S. supercomputing. Read more…

By Tiffany Trader

Russian Researchers Claim First Quantum-Safe Blockchain

May 25, 2017

The Russian Quantum Center today announced it has overcome the threat of quantum cryptography by creating the first quantum-safe blockchain, securing cryptocurrencies like Bitcoin, along with classified government communications and other sensitive digital transfers. Read more…

By Doug Black

Groq This: New AI Chips to Give GPUs a Run for Deep Learning Money

April 24, 2017

CPUs and GPUs, move over. Thanks to recent revelations surrounding Google’s new Tensor Processing Unit (TPU), the computing world appears to be on the cusp of Read more…

By Alex Woodie

DOE Supercomputer Achieves Record 45-Qubit Quantum Simulation

April 13, 2017

In order to simulate larger and larger quantum systems and usher in an age of “quantum supremacy,” researchers are stretching the limits of today’s most advanced supercomputers. Read more…

By Tiffany Trader

Messina Update: The US Path to Exascale in 16 Slides

April 26, 2017

Paul Messina, director of the U.S. Exascale Computing Project, provided a wide-ranging review of ECP’s evolving plans last week at the HPC User Forum. Read more…

By John Russell

Knights Landing Processor with Omni-Path Makes Cloud Debut

April 18, 2017

HPC cloud specialist Rescale is partnering with Intel and HPC resource provider R Systems to offer first-ever cloud access to Xeon Phi "Knights Landing" processors. The infrastructure is based on the 68-core Intel Knights Landing processor with integrated Omni-Path fabric (the 7250F Xeon Phi). Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Share This