OXNARD, Calif., Aug. 4, 2014 /PRNewswire-USNewswire/ -- The Allen
Institute for Brain Science, California
Institute of Technology, New York
University School of Medicine, the Howard Hughes Medical
Institute (HHMI) and the University of
California, Berkeley (UC Berkeley) are collaborating on a
project aimed at making databases about the brain more useable and
accessible for neuroscientists – a step seen as critical to
accelerating the pace of discoveries about the brain in health and
disease. With funding from GE, The Kavli Foundation, the Allen
Institute for Brain Science, the HHMI, and the International
Neuroinformatics Coordinating Facility (INCF), the year-long
project will focus on standardizing a subset of neuroscience data,
making this research simpler for scientists to share.
This is the first collaboration launched by "Neurodata Without
Borders," a broader initiative with the goal of standardizing
neuroscience data on an international scale, making it more easily
sharable by researchers worldwide. This first project is
called "Neurodata Without Borders: Neurophysiology."
Unlike image file formats such as jpeg or tiff, that store
digital information when we take a photo with our mobile phones and
allow us to share that photo with anyone with a computer, no such
data standard exists in neuroscience. However, developing such a
standard, or unified data format, would enhance the ability of
brain researchers worldwide to share and combine their research
results. This would not only drive progress in neuroscience but
also encourage the validation of existing results and create vital
new collaborations with other fields.
"Neuroscientists aren't limited by memory storage anymore; we're
limited by our ingenuity, the availability of data and our ability
to talk to each other," says Christof
Koch, Chief Scientific Officer at the Allen Institute. "This
pilot program is an effort to help us speak the same language."
Today, researchers can simultaneously record the electrical or
optical activity of a thousand neurons in a mouse's brain while the
animal is navigating a maze, for example, and that number may soon
be in the millions. These recent, rapid technical advances mean
that neuroscientists are generating data that is quantitatively and
qualitatively different than before. But the languages, or formats,
they use to capture those data (as well as the software tools they
use to access and analyze them) vary from laboratory to
laboratory—and sometimes even within a laboratory. This lack of
uniformity makes it challenging to share and integrate experimental
data—the raw material of science—and to mine and extract the most
value from them.
The need for a common data format in neuroscience is made more
urgent by the rise of large-scale collaborative projects, such as
the Brain Research through Advancing Innovative
Neurotechnologies (BRAIN) Initiative in the United States.
"These new initiatives are going to produce masses of data, but
if it isn't interchangeable and comparable, it's just not going to
be useful," says Koch.
On a practical level, scientific publishers and granting
agencies, such as the U.S. National Institutes of Health, are
moving toward mandating data sharing as a requirement for
funding.
"This is following on other efforts at openness in science,"
says Markus Meister, a professor of
biology at Caltech whose research group is supplying experimental
data to the project. "The idea is that the material or resources
that were developed with government funding or published in a
journal have to be made available. But for neurophysiology data,
there is no organized mechanism for doing that at the
moment."
The initial one-year program focuses on a subset of neuroscience
data: cell-based neurophysiology data, which is sought-after by
theorists who are building models of how the brain works. The
partners will work with software developers and vendors to
establish an open format that can store electrical and optical
recordings of neural activity, and, importantly, the conditions
under which an experiment was performed, such as how brain activity
was recorded, how the animal was behaving at certain time points,
and its species, sex and age. These "metadata" are often lost and
yet without them the research results are meaningless.
This "metadata problem" poses an enormous challenge, says
Friedrich Sommer, a theoretical
neuroscientist at UC Berkeley who oversees an existing repository,
CRCNS.org, where the neurophysiology datasets of Neurodata Without
Borders will be stored and shared. UC Berkeley is coordinating
Neurodata Without Borders with staff from the Allen Institute.
As Sommer explains, once a data format has been selected and
extended, the neurophysiology datasets will be translated into the
new common language and shared with the broader neuroscience
community through the repository. Lastly, "application programming
interfaces" (APIs) will be developed to allow researchers to use
the common format for their own data with ease.
To get to that point, Neurodata Without Borders is calling on
the neuroscience community to get involved. "We want
to solicit the best ideas for the data format, so we are
inviting researchers to look at the datasets which are now shared
in their current format at CRCNS.org. Our hope is to engage the
community to contribute ideas or propose their own data format for
consideration," says Sommer.
The most promising approaches to a common data format will be
discussed, tested and extended at Neurodata Without Borders
Hackathons, the first of which will be held in late November, to
drive the rapid development of innovative software tools.
"The project has an aggressive timeline, but in a year's time,
the goal is to come up with a standard for neurophysiology data
that we can agree on. We may not get it 100% right for 100% of
researchers, but we'll make a very good attempt," says
neuroscientist Karel Svoboda, group
leader at HHMI's Janelia Research Campus and a data-provider to
Neurodata Without Borders. "Then, by buying into the data format
ourselves—by explicitly moving our data into the format and making
them available, we'll set an example of how it could be done, and
hopefully have others in the neuroscience community follow in our
footsteps."
There have been smaller efforts to develop a common language for
neuroscience data in the past but they have fallen short of meeting
the goals of the new project.
"This new effort is not very different in spirit from past ones,
but it's at a much larger scale," says NYU School of Medicine's
Gyorgy Buzsaki, a pioneer of
data-sharing in neuroscience and another data-provider. "We're
trying to make Neurodata Without Borders as attractive as possible
by improving the quality of the datasets and how they are
documented, and by thinking hard about how best to help researchers
navigate around in them. Ultimately, if researchers can find and
access the data they're interested in in a few hours, they will
choose it. But that is a very difficult thing to do."
"With the emergence of large-scale brain initiatives around the
world, data reuse and sharing becomes more important than ever.
This project will facilitate neuroscience collaboration at a global
scale," says Sean Hill, Scientific
Director, INCF.
"Standardizing a subset of neuroscience data is vital to
accelerate the pace of research and innovation in brain health. We
are proud to be working with these best-in-class organizations on
such an important and needed study," says Robert Wells, executive director,
healthymagination strategy, GE.
Miyoung Chun, Executive Vice
President of Science Programs, The Kavli Foundation, agrees with
these assessments. "In neuroscience, as in many scientific fields,
there are massive amounts of 'Big Data' but no coherent way to
retrieve and use this information. Our hope is Neurodata Without
Borders: Neurophysiology is a major step toward changing this and
speeding breakthroughs in brain science."
ADDITIONAL INFORMATION:
Data: The first datasets from the participating
laboratories are already publicly available at CRCNS.org, a
repository of neuroscience data hosted by the Redwood Center for
Theoretical Neuroscience and the Helen Wills Neuroscience Institute
at UC Berkeley.
Hackathon: The first Neurodata Without Borders
Hackathon will be held at Janelia Farm, in Ashburn, Virginia, from November 20 –
22, 2014.
Developers who would like to participate should
contact: Fritz Sommer, fsommer@berkeley.edu
Researcher Queries: Researchers and research institutions
who wish to make queries about Neurodata Without Borders should
contact: Chris Martin,
cmartin@kavlifoundation.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.
ABOUT THE INSTITUTIONS
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 www.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.
GE. GE (NYSE: GE) works on things that matter. The
best people and the best technologies taking on the toughest
challenges. Finding solutions in energy, health and home,
transportation and finance. Building, powering, moving and helping
to cure the world. Not just imagining. Doing. GE works. For more
information, visit the company's website at www.ge.com.
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
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 www.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.
SOURCE The Kavli Foundation