UvA-DARE (Digital Academic Repository)

The Human Brain Project - Synergy between neuroscience, computing,

informatics, and brain-inspired technologies

Amunts, K.; Knoll, A.C.; Lippert, T.; Pennartz, C.M.A.; Ryvlin, P.; Destexhe, A.; Jirsa, V.K.;
D'Angelo, E.; Bjaalie, J.G.
DOI
10.1371/journal.pbio.3000344
Publication date
2019
Document Version
Final published version
Published in
PLoS Biology
License
CC BY
Link to publication

Citation for published version (APA):

Amunts, K., Knoll, A. C., Lippert, T., Pennartz, C. M. A., Ryvlin, P., Destexhe, A., Jirsa, V. K.,
D'Angelo, E., & Bjaalie, J. G. (2019). The Human Brain Project - Synergy between
neuroscience, computing, informatics, and brain-inspired technologies. PLoS Biology, 17(7),
Article e3000344. https://doi.org/10.1371/journal.pbio.3000344

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 COMMUNITY PAGE

The Human Brain Project—Synergy between

neuroscience, computing, informatics, and
brain-inspired technologies
Katrin Amunts ID1,2*, Alois C. Knoll3, Thomas Lippert ID4, Cyriel M. A. Pennartz ID5,
Philippe Ryvlin ID6, Alain Destexhe ID7, Viktor K. Jirsa8, Egidio D’Angelo9, Jan G. Bjaalie ID10
1 Institute for Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Germany, 2 C. and O. Vogt
Institute for Brain Research, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf,
Düsseldorf, Germany, 3 Institut für Informatik VI, Technische Universität München, Garching bei München,
a1111111111 Germany, 4 Jülich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich,
a1111111111 Germany, 5 Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, the
a1111111111 Netherlands, 6 Department of Clinical Neurosciences, Centre Hospitalo-Universitaire Vaudois (CHUV) and
a1111111111 University of Lausanne, Lausanne, Switzerland, 7 Unité de Neurosciences, Information & Complexité
a1111111111 (UNIC), Centre National de la Recherche Scientifique (CNRS), Gif-sur-Yvette, France, 8 Institut de
Neurosciences des Systèmes, Inserm UMR1106, Aix-Marseille Université, Faculté de Médecine, Marseille,
France, 9 Department of Brain and Behavioral Science, Unit of Neurophysiology, University of Pavia, Pavia,
Italy, 10 Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway

* [email protected]
OPEN ACCESS

Citation: Amunts K, Knoll AC, Lippert T, Pennartz

CMA, Ryvlin P, Destexhe A, et al. (2019) The Abstract
Human Brain Project—Synergy between
neuroscience, computing, informatics, and brain- The Human Brain Project (HBP) is a European flagship project with a 10-year horizon aim-
inspired technologies. PLoS Biol 17(7): e3000344.
ing to understand the human brain and to translate neuroscience knowledge into medicine
https://doi.org/10.1371/journal.pbio.3000344
and technology. To achieve such aims, the HBP explores the multilevel complexity of the
Published: July 1, 2019
brain in space and time; transfers the acquired knowledge to brain-derived applications in
Copyright: © 2019 Amunts et al. This is an open health, computing, and technology; and provides shared and open computing tools and
access article distributed under the terms of the
data through the HBP European brain research infrastructure. We discuss how the HBP cre-
Creative Commons Attribution License, which
permits unrestricted use, distribution, and ates a transdisciplinary community of researchers united by the quest to understand the
reproduction in any medium, provided the original brain, with fascinating perspectives on societal benefits.
author and source are credited.

Funding: This project has received funding from

the European Union’s Horizon 2020 Research and
Innovation Programme under Grant Agreement
No. 7202070 (HBP SGA1) and No. 785907 (HBP
SGA2). https://ec.europa.eu/programmes/ Introduction
horizon2020/en/h2020-section/fet-flagships The
To decode the multilevel brain’s complexity, the Human Brain Project (HBP) combines empiri-
funders had no role in study design, data collection
and analysis, decision to publish, or preparation of cal neuroscience in the human brain and in animals with theory and modeling, relying on and
the manuscript. developing advanced information and communication technology (ICT) including computing,
big data analytics, artificial intelligence (AI), and simulation [1]. The project represents a large-
Competing interests: The authors have declared
that no competing interests exist.
scale, interdisciplinary approach and consists of 12 subprojects—i.e., mouse brain organization,
human brain organization, systems and cognitive neuroscience, theory, neuroinformatics,
Abbreviations: ADNI, Alzheimer’s Disease
brain simulation, medical informatics, high-performance analytics and computing, neuro-
Neuroimaging Initiative; AI, artificial intelligence;
Brain/MINDS, Brain Mapping by Integrated
morphic computing, neurorobotics, administrative support, and ethics and society. Knowledge
Neurotechnologies for Disease Studies; CLSM, and constraints in neuroscience are drivers for developing research platforms through a code-
confocal laser scanning microscopy; EEG, sign process. This has proven to be a very successful approach for transdisciplinary work in the

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electroencephalography; FAIR, Findable Accessible HBP. Through codesign, the HBP is developing and releasing a unique European brain research
Interoperable Re-usable; FENIX, Federated infrastructure. To enable neuroethical analysis and develop, broaden, and enhance responsible
Exascale Network for data Integration and
research and innovation, the HBP was one of the first initiatives worldwide to establish a dedi-
eXchange; GDPR, General Data Protection
Regulation; HBP, Human Brain Project; HLST, cated subproject for ethics.
High-Level Support Team; IBI, International Brain
Initiative; ICT, information and communication Neuroscience: Understanding the brain at multiple scales
technology; MIP, Medical Informatics Platform;
MNI, Montreal Neurological Institute; PLI, polarized The multiscale approach of the HBP links experiments conducted at the molecular, subcellu-
light imaging; TEM, transmission electron lar, and cellular levels and at the level of neuronal populations and macroscopic regions, up to
microscopy; TPFM, two-photon fluorescence large-scale networks and behavior. Research on mouse brain organization primarily gathers
microscopy. structural and physiological data at the subcellular and cellular levels, which is critical for bio-
Provenance: Not commissioned; externally peer physically detailed modeling and simulations. For instance, novel data on microcircuits in the
reviewed cerebellum shed new light on its function, including forward and feedback control [2].
Electron microscopy, two-photon and light-sheet imaging, polarized light imaging (PLI),
and diffusion MRI, along with advanced electrophysiological techniques including patch
clamping and multielectrode array recordings in vitro and in vivo as well as electroencephalog-
raphy (EEG), provide data on the connectome on the different spatial and temporal scales (Fig
1). These data, together with those on the cellular and molecular organization, functional and
connectivity data, and many more, are integrated into the HBP Brain Atlases, which provides

Fig 1. Multiscale organization of brain connectivity. Different methods are being used in the HBP to analyze neuronal connections from the nanometer scale to
the centimeter scale. Although TEM/SEM (e.g., Rodriguez-Moreno and colleagues [5]) and CLSM/TPFM (e.g., Silvestri and colleagues [6]) can image subcellular
structures, including synapse, with great detail, they cannot cover the whole human brain. 3D-PLI has a spatial resolution down to 1.3 μm, which resolves most of
the myelinated fibers, and has the potential to image the whole human brain (e.g., Axer and colleagues [7]). Diffusion MRI is an in vivo method covering the whole
brain, but with limited spatial resolution, which does not resolve single nerve fibers (e.g., Beaujoin and colleagues [8]). The possibility to link these different data
shows the great advantage of HBP—it facilitates the combination of approaches at scale, backed by high-performance computing and the data exchange
infrastructure FENIX. CLSM, confocal laser scanning microscopy; FENIX, Federated Exascale Network for data Integration and eXchange; HBP, Human Brain
Project; PLI, polarized light imaging; TEM, transmission electron microscopy; TPFM, two-photon fluorescence microscopy. Figure elements provided by Markus
Axer.
https://doi.org/10.1371/journal.pbio.3000344.g001

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 a basis for human and rodent brain research [3]. The atlases also establish the structural frame
for modeling and simulation studies, which is a unique feature of the HBP approach. For
example, simulations use patient-specific brain connectivity and imaging of malformations to
personalize network models for seizure prediction and surgery [4].
Understanding the brain at multiple scales requires the integration of anatomy and physiol-
ogy with cognitive and systems neuroscience to flesh out the neural mechanisms underlying
cognition—e.g., in object recognition, visuomotor control, episodic memory, sleep, wakeful-
ness, and consciousness. To this end, researchers combine experimental studies in rodents and
humans, integrate data in computational models and simulations of large-scale neuronal net-
works, and simplify and apply these models to control physical robots or simulated agents in
order to capture essential features of animal and human behavior. Neuroscientists working on
the cellular or molecular level exchange results with researchers working in cognitive and sys-
tems as well as theoretical neuroscience to cast neurobiological principles into new theories
and formal models, which then prompt simulation studies and the development of neuro-
morphic computing systems. There is still no comprehensive theory describing information
processing in the brain, but important building blocks can be won through these approaches
and may constitute the basis for such a theory in the future.

The European brain research infrastructure

This infrastructure consists of different components—neuroinformatics, simulation, high-per-
formance analytics and computing, neuromorphic computing, and neurorobotics. To enable
interdisciplinary research, a seamless transition and integration of the different components
and data is necessary. Collaborating with the neuroscience branches, the HBP is developing
and providing workflows, from organizing and storing data and making them accessible
according to the Findable Accessible Interoperable Reusable (FAIR) data principles [9] to data
analysis, modeling, simulation, and brain-inspired technologies (Fig 2).
In addition, the voucher system of the HBP allows researchers outside the project to request
innovation support or technical support for the modification of tools and workflows to meet
their needs, thus facilitating broader uptake of the integrated platform services.
The High-Level Support Team (HLST) of the HBP is available for answering questions or
resolving issues with the use of the tools and services and for adapting tools and workflows for
specific use cases. Specifically, researchers outside HBP can make their data discoverable and
accessible in the Knowledge Graph and Atlases by applying for access to curation services and
data storage through the HLST. The HLST help desk and ticketing system is available at the
following e-mail: [email protected].
Various types of neuroscience data are being generated, with differences in format, meta-
data, or level of precision. Through a curation process, metadata are assigned and stored in the
HBP Knowledge Graph, an online graph database allowing advanced searches (Fig 2).
Thereby, data and models become findable and interpretable. Data can be downloaded or used
directly in workflows available through the computing infrastructure, with terms of use and
licenses defined for all available data sets. Data are also being made available through the
Knowledge Graph with integrated multilevel HBP Atlases, holding information about the
brain in standard reference spaces. The Human Brain Atlas supports different reference spaces
including the T1-weighted, single-subject template of the Montreal Neurological Institute
(MNI) [10] and the BigBrain [11]. The atlases are more and more populated with data from
the different fields to form fully interoperable, multimodal representations of the human and
rodent brain. They are compatible with other resources [12] and capable of integrating data
not only from healthy subjects but also from patients.

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 Fig 2. The HBP integrated platform. Research data from experiments, models, or simulations are uploaded to data storage at
the HBP high-performance computing centers. The data are tagged with metadata through a 3-tier curation process covering
basic metadata, metadata connecting the data to the HBP Atlases, and additional detailed metadata depending on the data
modality. The data are made accessible for users through searches for metadata (“Faceted data search” or “Spatial search”) in the
online HBP Knowledge Graph and HBP Atlases. The “Search results” give access to collections of data accompanied by
information about the project they belong to, the experimental methods used to produce the data, the terms of use, and the
citation requirements for use of the data. In the present implementation, users can (1) download the data, (2) inspect the data
using an online atlas viewer or a virtual microscopy tool showing image data with atlas overlays and spatial coordinates, or (3)

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 analyze the data using the “Tools and workflows for viewing and analysis” accessible through the HBP Collaboratory, the portal
to the use of HBP tools and services, or directly through the atlas for some cases. The HBP Knowledge Graph and HBP Atlases
are openly available at https://www.humanbrainproject.eu/en/explore-the-brain/. Accounts for use of the HBP Collaboratory can
be requested at https://services.humanbrainproject.eu/oidc/login. HBP, Human Brain Project. Image credits: doi:10.1371/journal.
pone.0118277, doi:10.1371/journal.pbio.1002383, doi:10.1371/journal.pbio.1000173 (based on a dataset available at doi:10.12751/
g-node.f83565).
https://doi.org/10.1371/journal.pbio.3000344.g002

The Medical Informatics Platform (MIP) exploits new ICT in the context of clinical neuro-
sciences [13]. It combines local components installed in every participating hospital and a web-
based central node connecting the local components. Its architecture enables the extraction,
processing, and analysis of medical data collected during either clinical practice or research.
The MIP allows the automatic generation of brain regional volumes from T1 MRI data. The key
is to enable General Data Protection Regulation (GDPR)-compliant federated analysis of dis-
tributed clinical datasets without moving the data out of the hospital, a crucial issue in the con-
text of data privacy concerns and regulations. This unique feature opens the way for studies of
unmatched scale, keeping in mind that 165 million European citizens suffer from brain diseases.
A first proof-of-concept study in the field of dementia collected >6,000 datasets from three hos-
pitals and analyzed them together with data from Alzheimer’s Disease Neuroimaging Initiative
(ADNI). The future MIP will include many more hospitals and consider data from patients
with epilepsy, traumatic brain injury, and behavioral disorders. It offers an ideal infrastructure
to implement AI-based diagnostic and patient management tools for clinical practice in con-
junction with modeling and simulation efforts in personalized medicine.
Some of the research data in brain science already reach the petabyte range. The HBP stor-
age at high-performance computing centers in Europe, the FENIX infrastructure, enables
researchers to upload their data and use high-end simulation and processing of big data in an
easy and straightforward way from wherever they are. To bring neuroscientists to supercom-
puting is one of the aims of the HBP; it opens new ways to solve neuroscientific questions
requiring significant compute resources. Computer specialists benefit from neuroscience use
cases, which are instrumental to identify the characteristics of future, extreme-scale computers
including modular supercomputers. Already, the integrated platform of the HBP is the first
research infrastructure that is embedding two worldwide, unique neuromorphic computing
machines with novel non–von Neumann computing architecture (SpiNNaker and Brain-
ScaleS) into user workflows [14]. This powerful computing infrastructure will smoothly handle
complex workflows, combining, for example, compute-intensive simulation with the analysis
of data using deep learning.
Neurorobotics is a brain-inspired technology; a novel interdisciplinary field of science at
the confluence of neuroscience, robotics, and artificial intelligence; and part of the research
infrastructure. It recognizes the fact that the brain is embedded into a body and that this body
is itself embedded into a dynamic environment. This approach considers that environmental
interactions cannot be ignored to faithfully simulate the brain and understand behavior. This
embodiment (through either a simulated agent or a physical robot) provides neuroscientists
with a new experimental paradigm to test their neural models [15]. Simulations implementing
closed-loop experiments in neurorobotics encompass the full action–perception–cognition
loop. Observation of brain activity and physical performance in the context of relevant behav-
ioral tasks then enables researchers to either refute or support the theory behind their neural
models, thus uniquely informing their scientific investigations. This line of research will even-
tually lead to a new paradigm, “closed-loop neuroscience,” for which the HBP intends to pro-
vide the necessary infrastructure. Such an example illustrates the synergistic relationship
between neuroscience, ICT, and brain-like computing within HBP.

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 The brain research infrastructure will unify the individual components into one cloud-
based superstructure, facilitating the exchange of knowledge, data, models, and algorithms
within HBP as well as between the HBP and the “outside world.” Research infrastructures in
other fields, such as particle physics, served as role models to create active, tangible interfaces
between researchers and the infrastructure.

Concluding remarks
The HBP is pursuing an open-science approach. Simulation engines, models, analysis tools, data,
and the HBP Atlases are shared with the community through a web-based system as a common
entry point. Multilevel brain complexity is a challenge that needs a sustainable and strong—but
also flexible—research infrastructure at the interface of neuroscience and computing, which is
developed by the project. It offers and develops services to the research community to solve scien-
tific problems from various fields including FAIR data; atlasing; medical brain activity data; web-
based, interactive supercomputing; closed-loop neuroscience; robotics and AI; and modeling and
simulation workflows. The HBP approach has already led to a significant number of break-
throughs, among them the development of novel spike-based learning algorithms, which were
implemented on neuromorphic computers with the aim of obtaining general-purpose tools for a
new generation of AI applications; innovative theoretical models that made use of results from
experimental neuroscience addressing the multiscale organization of the brain; and significant
advances in understanding the neural basis of learning and perception [16], spatial memory [17],
multisensory integration [18], and sleep and consciousness [19]. These are a few examples illus-
trating that the integration of neuroscience and ICT within a common framework opens new
ways toward a better understanding of brain complexity. (For a regularly updated overview, see
https://www.humanbrainproject.eu/en/science/highlights-and-achievements/.)
A research culture of collaboration and data sharing, which is accompanied by activities
addressing ethical and philosophical issues and their societal implications, has been key for the
HBP from the very beginning. The HBP infrastructure provides a concrete basis to collaborate
with the wider, international research community. It is linking the European project into an
international context—e.g., through the International Brain Initiative (IBI). The IBI was cre-
ated in 2017 with the Australian Brain Alliance, Japan Brain Mapping by Integrated Neuro-
technologies for Disease Studies (Brain/MINDS) Project, Korea Brain Initiative, the European
HBP, and the United States Brain Initiative as the initial members. It has the aim of coordinat-
ing efforts between the global initiatives to speed up progress on decoding the brain’s code.

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