Apr 27, 2020

PRP Boosts Inter-Campus Collaboration on Brain Research

Using the Pacific Research Platform, researchers at three US universities — University of California Santa Cruz, University of California San Francisco, and Washington University in St. Louis — collaborate to transfer, share, and analyze multi-terabyte- to petabyte-size datasets as part of work to better understand the human brain.

Researchers at one campus upload open-source data while partners at another campus provide analysis and machine learning, and both meet seamlessly on the PRP, drastically accelerating experiment times — sometimes from weeks to hours. The easily accessible, cloud-scale PRP enables standard tools, scalable processing, streaming solutions, automated analysis, and remote experimentation controls.

The PRP is a partnership of more than 50 institutions, led by researchers at the University of California at San Diego and Berkeley. PRP has support from the National Science Foundation, and includes the US Department of Energy’s Energy Science Network (ESnet), as well as scores of research universities in the nation and around the world. The PRP builds on the optical backbone of Pacific Wave, a joint project of CENIC and the Pacific Northwest Gigapop (PNWGP), to create a high-speed, big-data “superhighway” that enables collaboration in a broad range of data-intensive fields. Interest in the PRP has sparked scaling up the project to a full National Research Platform (NRP) and, indeed, a Global Research Platform (GRP).

During a monthly NRP webinar series that highlights PRP and NRP success stories, David Parks, a researcher and doctoral student in biomolecular engineering in the Braingeneers Lab at UCSC, presented ways he uses the PRP for cross-campus collaboration. Parks, whose focus is on deep learning technologies, works with researchers at UCSC, UCSF, and WashU to scale up and provide analysis on their neuroscience experiments. About 100 researchers and computer scientists attended the webinar in March to learn how the PRP and NRP can support more ambitious research and realize new innovations.

“The PRP’s cyberinfrastructure shows the transformative power of uniting campuses and providing a platform for the ubiquitous flow of knowledge for research collaboration,” said PRP Principal Investigator Larry Smarr.

Understanding the Neuroscience of Sleep

In the Hengen Lab at WashU, researchers study how different parts of the brain influence sleep. Electrodes connected to the brains of live mice record months of data. The electrodes record neural spikes in individual cells in the mouse’s brain, with each spike providing a signature pattern for that cell. Recordings are conducted at a rate of 25,000 samples per second, and recordings are taken on more than 500 electrodes at a time. The brain-machine interfacing technology is similar to that used by Elon Musk’s Neuralink.

WashU researchers upload these massive datasets via Internet2’s national research and education network and the regional PRP, and Parks applies machine learning techniques to the information. By training a neural network on the PRP’s machine learning-optimized compute cluster (Nautilus), Parks helps researchers to predict whether the mouse is awake, in REM sleep, or in non-REM sleep. “Before using PRP, it took a week just to transfer a 100 GB dataset between campuses,” Parks said. “Now, the Hengen Lab can fire off a copy command, and the next morning a 3 TB dataset is online, and I'm putting a compute job on there that's making use of that data. That can happen within 12 hours.”

The Hengen Lab can transfer terabytes of raw neural data through the S3 interface to the PRP and NRP, where David Parks at the Braingeneers Lab provides machine learning techniques to analyze the data, and results are sent back to the Hengen Lab within mere hours or days. Source: David Parks, March 2020.

Examining the Evolution of the Human Brain

At WashU, UCSC, and UCSF, researchers collaborate to grow and study organoid cell cultures of human glial neural cells to learn about the formation of the brain’s complex circuitry. Researchers have made important discoveries, including how genetic changes in evolution gave humans larger, differently-wired brains. Similar to the mouse recordings, electrodes connected to each organoid can produce datasets that reach into the terabyte scale.

PRP and NRP enable researchers at the three universities to scale up experimentation so that hundreds or even thousands of experiments can be conducted in parallel. “Working with one organoid, one data point, doesn’t provide a lot to learn from,” Parks said. “But if you scale that up to work with dozens of organoid recordings at the same time, you can do experimentation at a much higher scale.” The Braingeneers are automating experimentation with controls from remote devices, such as smartphones and Internet of Things (IoT) interfaces, which are directly connected to the PRP. “The goal is to get to the point where nobody has to be in the lab to control an experiment,” he said.

Deploying An Accessible Big Data Platform

PRP runs the web service interface Amazon Simple Storage Service (S3); the file system Ceph, with storage distributed across hundreds of PRP nodes worldwide; the container platform Docker; and Google’s Kubernetes container orchestration system. “It’s a nice federated model - a simple model for any research team that doesn’t have all the technical knowledge for implementing something large scale,” Parks said. “Accessing S3 is simple and anybody can learn it. You don’t have to be a computer scientist. For data analysis, you just need someone capable of learning a bit of Docker.”

PRP is the model for big data collaboration. The platform supports a broad range of data-intensive research projects that will impact science and technology worldwide, including projects on galaxy formation and evolution, telescope surveys, particle physics data analysis, simulations for earthquakes and natural disasters, climate modeling, and virtual reality and ultra high-resolution video development.

Watch the monthly webinar series to discover more success stories like Parks’.

Watch the presentation, “The National Research Platform: An Update on Progress Towards Scaling," from CENIC’s Annual Conference.

Other PRP Success Stories

• Big Data: How the PRP Enables Scientists to Unlock Genetic Secrets
• Rivers in the Sky: How PRP Enables Scientists to Predict Extreme Weather
• Identifying Tiny Organisms with Giant Impact on Climate

About Internet2® • www.internet2.edu

Internet2® is a non-profit, member-driven advanced technology community founded by the nation’s leading higher education institutions in 1996. Internet2 serves 320 US universities, 60 government agencies, 43 regional and state education networks and through them supports more than 100,000 community anchor institutions, over 1,000 InCommon participants, and 54 leading corporations working with our community, and 70 national research and education network partners that represent more than 100 countries.

Internet2 delivers a diverse portfolio of technology solutions that leverages, integrates, and amplifies the strengths of its members and helps support their educational, research, and community service missions. Internet2’s core infrastructure components include the nation’s largest and fastest research and education network that was built to deliver advanced, customized services that are accessed and secured by the community-developed trust and identity framework.

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