Berkeley Lab Researchers to Build Standards for Neurophysiology Data
$2 Million NIH Grant to Fund Neurodata Without Borders Project
November 20, 2018
Researchers from the Lawrence Berkeley National Laboratory (Berkeley Lab) and the Allen Institute for Brain Science will receive $2 million from the National Institutes of Health (NIH) to develop a next-generation data format and software ecosystem for the Neurodata Without Borders: Neurophysiology (NWB:N) project.
NWB:N is a consortium of researchers and foundations that are interested in breaking down obstacles to data use and sharing in neuroscience. The group ultimately aims to standardize neurophysiology data on an international scale to ensure the success of brain research worldwide and accelerate the pace of scientific discovery.
With funding from the Kavli Foundation, Berkeley Lab scientists Oliver Ruebel, Andrew Tritt and Kristofer Bouchard led the development of the beta version of NWB:N 2.0, and will continue to advance the development of NWB:N as part of the NIH BRAIN Initiative. This work has been in close collaboration with UC San Francisco’s Loren Frank and Eddie Chang, Lydia Ng and others from the Allen Institute for Brain Science, the NWB:N Executive Board members and the broader NWB:N community.
As NWB:N 2.0 moves toward a full release at the end of this year, the team presented a poster of its work at the 2018 Society for Neuroscience meeting in San Diego, CA on November 6. With the new NIH funding, Ruebel and his colleagues will develop and maintain an accessible and sustainable software ecosystem for NWB:N. They will also design methods for integrating standard vocabularies and data provenance with NWB:N and develop standards for integration of NWB:N with data management systems and tools for community extensions and adoption.
“The lack of standards for neurophysiology data and related metadata is the single greatest impediment to fully extracting return-on-investment from neurophysiology experiments, impeding interchange and reuse of data and reproduction of derived conclusions,” said Bouchard, a research scientist in Berkeley Lab’s Biological Systems and Engineering Division. “The high-value datasets collected as part of the BRAIN initiative should be made widely available to the research community. Unfortunately, the output of neurophysiology research is currently almost exclusively research papers, with the original data and analysis tools rarely available.”
Berkeley Lab’s leadership in the NWB:N development would have not been possible without the Laboratory Directed Research and Development (LDRD) project BRAINformat: A Data Standardization Framework for Neuroscience Data, Reubel emphasized.
“BRAINformat allowed us to engage with the neuroscience community and present our concepts and really was the starting point for our engagement with NWB:N,” said Reubel, a research scientist in Berkeley Lab’s Computational Research Division (CRD) and principal investigator on the NIH project.
The team subsequently began working on a 2.0 version of NWB:N and released a first beta version of NWB:N 2.0 last year so that users could offer input before the version’s officially release this year. Berkeley Lab also hosted a user engagement hackathon earlier this year, bringing together users to help them adopt NWB:N.
“We used modern software engineering principles to develop NWB:N 2.0. We incorporated a new modular software architecture and application programming interfaces that allow users to efficiently interact with the NWB:N data format, files and specifications,” said Tritt, a computer systems engineer in CRD and principle software architect on the NIH project.
“Despite these innovations, substantial software development remains to fully deliver on NWB:N’s promise of standardizing neurophysiology data on an international scale, and we are excited to tackle several key challenges as part of our work with the NIH BRAIN Initiative, ” said Ruebel.
For more information about Berkeley Lab’s Contributions to Neurodata Without Borders:
- Berkeley Lab Hosts Neurodata Without Borders Hackathon: https://cs.lbl.gov/news-media/news/2018/berkeley-lab-hosts-neurodata-without-borders-hackathon/
- Beta of Neurodata Without Borders Software Now Available: https://cs.lbl.gov/news-media/news/2017/beta-of-neurodata-without-borders-software-now-available
- A Standard for Neuroscience Data: http://cs.lbl.gov/news-media/news/2014/a-standard-for-neuroscience-data/
About Computing Sciences at Berkeley Lab
The Computing Sciences Area at Lawrence Berkeley National Laboratory(Berkeley Lab) provides the computing and networking resources and expertise critical to advancing Department of Energy Office of Science (DOE-SC) research missions: developing new energy sources, improving energy efficiency, developing new materials, and increasing our understanding of ourselves, our world, and our universe. ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 7,000-plus scientists at national laboratories and universities. NERSC and ESnet are both Department of Energy Office of Science National User Facilities. The Computational Research Division (CRD) conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation.
Berkeley Lab addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the DOE’s Office of Science. The DOE Office of Science is the United States' single largest supporter of basic research in the physical sciences and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.