Neuroscientists, funders launch resource aimed at breaking data barriers in brain research
An alliance of brain researchers and funders has announced a common data format to facilitate the free and open exchange of complex information about the brain–information that scientists can then use to accelerate progress in understanding the brain and developing new treatments for brain disorders.
The new format, known as Neurodata Without Borders (NWB): Neurophysiology, is the first widely available format that allows researchers to capture and share data generated by two of the most widely used methods in brain research: optical and electrical neurophysiology. A description of the format and its potential impact on the field of neuroscience was published online Nov. 18 in the journal Neuron.
"A unified data format is prerequisite to really achieving breakthroughs in understanding the brain," said Fritz Sommer, a neuroscientist at the Redwood Center for Theoretical Neuroscience and Helen Wills Neuroscience Institute, University of California, Berkeley (UC Berkeley), and senior author on the paper. "It's hard to overstate the importance of new tools that will allow neuroscientists to share, search, analyze and integrate the large, complex data sets that are the product of modern neurophysiology experiments. The NWB format enables such tools to be developed."
New research approaches, developed in the last decade, are profoundly altering the way neuroscientists study the brain, a trend that is accelerating due to President Obama's Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. Scientists can now ask questions about how the brain functions at the level of brain circuits and networks by recording the simultaneous activity of hundreds, even thousands, of brain cells in live animals. As a result, neuroscience data sets have become extremely large and complex — capturing a suite of experimental different variables — and it has become a major challenge to manage those data and extract meaning from them.
"It's of the utmost importance that neuroscience arrives at a standard, as other fields such as astronomy and genomics have, so that there's a way to compare and to contrast experimental data," said Christof Koch, President and Chief Scientific Officer of the Allen Institute for Brain Science in Seattle and one of the researchers who initiated the project. "Our current tools generate an abundance of data in different formats that are not easily transcribed from one into the other, yielding a Tower of Babel situation. Thanks to NWB, we can now easily read and analyze data streaming in from different instruments to understand the underlying logic."
As the World Wide Web developed, software developers adopted standards for web pages so that they could be viewed consistently in different browsers. Similarly, the NWB format ensures that neuroscientists around the world can access, share, compare and analyze cellular-based neurophysiology data sets, which are essential to studying the connection between brain function and behavior.
The NWB:Neurophysiology format expands neuroscientists' toolkit in two ways: First, it encodes both raw data and related metadata, which describe the experimental conditions under which the data were produced, for optical and electrical recordings of the brain in action. That combination is important because existing standards focus on electrical recordings, which limits the ability of neuroscientists to integrate their data. Second, it is extensible, therefore it can be modified to capture other types of neurophysiology data, such as imaging data.
"Currently, there are almost as many data formats as major neurophysiology laboratories. In addition to a common format, NWB:Neurophysiology also places a strong emphasis on providing sufficient metadata. Oftentimes it is impossible to figure out whether recordings were made from male or female animals, from the right or left hemisphere of the brain, or the time of recording, even in published papers. Information of this kind will be extremely valuable when meta-analyses on many data sets will be performed. Even if the NWB format changes over the years, the desire of an agreed format is made very clear by our effort," said György Buzsáki of New York University and a scientific partner of the NWB:Neurophysiology project.
The Neurodata Without Borders alliance launched in mid 2014 to break down the obstacles to data sharing. The NWB:Neurophysiology data format is the result of a dedicated, one-year pilot project. It was created by software developers and theoretical and experimental neuroscientists from UC Berkeley and the Allen Institute for Brain Science, György Buzsáki of New York University, Markus Meister of the California Institute of Technology, and Karel Svoboda of the Janelia Research Campus of the Howard Hughes Medical Institute (HHMI).
These scientific partners have publicly released multiple large, web-based data sets in the NWB:Neurophysiology format, including the Allen Institute's Cell Types Database, which contains detailed information about hundreds of individual cells in the mouse brain.
"I'm really proud of the fact that we have this format and that it was created in such a way that we can continue to build on it. It's much more than anything that we had before," said Chinh Dang, Chief Administrative Officer at the Allen Institute.
The NWB team will continue to refine the data format and develop new analysis tools to maximize its usefulness, in partnership with the neuroscience community.
"Would it not be wonderful to have a 'Neurophysiology DropBox' into which investigators could simply drop their recordings and share with everyone? We are not there yet but the NWB program is steering us in that direction. Agreeing on a format facilitates this sender-receiver communication," said Buzsáki.
"Real understanding of the brain and its diseases can only come from the whole world being engaged in the challenge. The NWB format is a key step to enable collaborative research on the brain," said Linda Lanyon, Executive Director, and Sean Hill, Scientific Director, INCF.
Funding and support for NWB:Neurophysiology was provided by the Allen Institute, GE Healthymagination, the International Neuroinformatics Coordinating Facility (INCF), HHMI and The Kavli Foundation.
"We are delighted by the progress made by these outstanding researchers and we're confident that this new format will make a significant contribution to better understanding the brain," said Robert Wells, Executive Director for Strategy, GE Healthymagination. "GE is proud to have been a supporter of this important initiative."
"This is such an exciting time for brain research. But there are still hurdles to overcome to understand the brain. We hope that neuroscientists will embrace the NWB data standard and improve it so that the full impact of their creativity and ingenuity can be felt," said Miyoung Chun, Executive Vice President of Science Programs at The Kavli Foundation.
For more information about the NWB:Neurophysiology format, including technical specifications, or to request a preprint of the Neuron article, visit NWB.org.
About Neurodata Without Borders
Neurodata Without Borders (NWB) is an initiative aimed at standardizing neuroscience data on an international scale. Established in response to the U.S. Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative, the goal is to break the geographic, institutional barriers, technological and policy barriers that impede the flow of neuroscience data to the broad scientific community. This is seen as key to accelerating the pace and success of brain research worldwide.
Neurodata Without Borders: Neurophysiology (NWB:N) is a pilot project to produce a unified data format for cellular-based neurophysiology data. The NWB:N team consists of neuroscientists and software developers who recognize that adoption of a unified data format is an important step toward breaking down the barriers to data sharing in neuroscience. It is funded by GE, the Allen Institute for Brain Science, the Howard Hughes Medical Institute HHMI, The Kavli Foundation and the International Neuroinformatics Coordinating Facility. Its founding scientific partners are the Allen Institute, the Svoboda Lab at the Janelia Research Campus of HHMI, the Meister Lab at the California Institute of Technology, the Buzsáki Lab at New York University School of Medicine and the University of California, Berkeley.
Allen Institute for Brain Science
The Allen Institute for Brain Science is an independent, 501(c)(3) nonprofit medical research organization dedicated to accelerating the understanding of how the human brain works in health and disease. Using a big science approach, the Allen Institute generates useful public resources used by researchers and organizations around the globe, drives technological and analytical advances, and discovers fundamental brain properties through integration of experiments, modeling and theory. Launched in 2003 with a seed contribution from founder and philanthropist Paul G. Allen, the Allen Institute is supported by a diversity of government, foundation and private funds to enable its projects. Given the Institute's achievements, Mr. Allen committed an additional $300 million in 2012 for the first four years of a ten-year plan to further propel and expand the Institute's scientific programs, bringing his total commitment to date to $500 million. The Allen Institute's data and tools are publicly available online at brain-map.org.
California Institute of Technology
Caltech is a world-renowned research and education institution focused on science and engineering, where faculty and students pursue new knowledge about our world and search for the kinds of bold and innovative advances that will transform our future. Caltech's neuroscience research spans a vast range of subjects and the integration of approaches from many disciplines.
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Howard Hughes Medical Institute
The Howard Hughes Medical Institute plays a powerful role in advancing scientific research and education in the United States. Its scientists, located across the country and around the world, have made important discoveries that advance both human health and our fundamental understanding of biology. The Institute also aims to transform science education into a creative, interdisciplinary endeavor that reflects the excitement of real research.
International Neuroinformatics Coordinating Facility
The International Neuroinformatics Coordinating Facility (INCF) is an international organization launched in 2005, following a proposal from the Global Science Forum of the Organisation for Economic Co-operation and Development (OECD) to establish international coordination and collaborative informatics infrastructure for neuroscience – and currently has 17 member countries across North America, Europe, Australia and Asia. INCF establishes and operates scientific programs to develop standards for neuroscience data sharing, analysis, modeling and simulation while coordinating an informatics infrastructure designed to enable the integration of neuroscience data and knowledge worldwide and catalyze insights into brain function in health and disease.
The Kavli Foundation
The Kavli Foundation advances science for the benefit of humanity, promotes public understanding of scientific research, and supports scientists and their work. Based in Southern California, the Foundation's mission is implemented through an international program of research institutes in the fields of astrophysics, nanoscience, neuroscience and theoretical physics, and through the support of conferences, symposia, endowed professorships and other activities. The Foundation is also a founding partner of the biennial Kavli Prizes, which recognize scientists for their seminal advances in three research areas: astrophysics, nanoscience and neuroscience. For more information, visit http://www.kavlifoundation.org.
New York University School of Medicine
NYU Langone Medical Center, a world-class, patient-centered, integrated academic medical center, is one of the nation's premier centers for excellence in clinical care, biomedical research, and medical education. The Medical Center's tri-fold mission to serve, teach, and discover is achieved 365 days a year through the seamless integration of a culture devoted to excellence in patient care, education, and research. In 2011, NYU Langone Medical Center established a new, state-of-the-art Neuroscience Institute to leverage NYU's excellence in both basic science and clinical medicine. The Neuroscience Institute will play a unifying role to enhance communication and collaboration among clinical, translational, and basic neuroscientists. For more information, go to NYULMC.org, and interact with us on Facebook, Twitter, and YouTube.
University of California, Berkeley
UC Berkeley is the world's premier public university with a mission to excel in teaching, research and public service. This longstanding mission has led to the university's distinguished record of Nobel-level scholarship, constant innovation, a concern for the betterment of our world, and consistently high rankings of its schools and departments. The campus offers superior, high value education for extraordinarily talented students from all walks of life and a commitment to the competitiveness and prosperity of California and the nation.