Human Brain Project Specific Grant Agreement 2

Project Information

HBP SGA2

Grant agreement ID: 785907

DOI

10.3030/785907

Project closed

EC signature date 3 May 2018

Start date 1 April 2018

End date 31 March 2020

Funded under

• EXCELLENT SCIENCE - Future and Emerging Technologies (FET)

Total cost

€ 88 000 000,00

EU contribution

€ 88 000 000,00

Coordinated by

ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Switzerland

Periodic Reporting for period 1 - HBP SGA2 (Human Brain Project Specific Grant Agreement 2)

Reporting period: 2018-04-01 to 2020-03-31

Summary of the context and overall objectives of the project

Understanding human brain organisation at all relevant levels is a big challenge, yet this must be done to improve treatment of brain disorders, create new computing technologies and provide insight into our humanity. The HBP’s unique strategy develops cutting-edge ICT to gather, integrate and analyse brain data, understand the brain, healthy or diseased, and emulate its unique computational capabilities. By sharing our tools and data, we aim to catalyse collaboration and accelerate progress in these fields.
Unlocking the brain’s secrets promises major scientific, social and economic benefits. One is improved diagnosis and treatment of brain disorders; a growing health burden in our ageing population. A second is neuroscience’s potential to contribute to future ICT, including extreme-scale, modular and neuromorphic computing, and neurorobotics.
The HBP studies the brain at different levels, from genomics to higher-level brain functions. It builds an ICT-based research infrastructure to facilitate worldwide research cooperation and sharing of software tools, data and models, based on FAIR principles. Our co-design approach, where neuroscientists, engineers and computer experts work together, ensures that our infrastructure meets real research needs. We facilitate researchers’ secure access to large sets of patient data to accelerate medical research. The HBP trains scientists to use its tools and educates young scientists to work across disciplines. It also incorporates an unprecedented responsible research and innovation programme, with public engagement, philosophical reflection on research and assessment of its societal implications of research and ethics support, including regulatory compliance. It is Europe’s leading integrator of and contributor to global brain research efforts.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The HBP has created a large collection of curated multi-level, multi-species data, tools and models, from single neurons to whole brain, which will make EBRAINS a unique community resource. Multimodal approaches, across species and methodologies, have provided unprecedented insight into brain organisation at different levels. The HBP Atlas provides access to ultra-high resolution anatomical data in the BigBrain, plus proof-of-concept using iEEG data via Hibop, and a link to The Virtual Brain simulation/modelling support. This allowed fusing computational modelling, deep learning, experimentation and robotics to understand how the brain coordinates visually-guided actions, resulting in a new closed-loop architecture for robotic systems. Developed to support drug discovery, a first automated GPCR-tailored protocol connecting molecular and subcellular levels enabled prediction of ligand binding at subcellular level. Integration of molecular properties was also shown in large-scale mouse brain cellular simulations, run on HPC resources provided by Fenix. A framework was developed for assessing consciousness and brain complexity in human, rodent and in silico brains.
EBRAINS made selected services available to external users. The Neuroinformatics Platform improved input into the Knowledge Graph; its data and models content tripled in the last 12 months. The brain atlases were updated to cover more regions, template spaces and modalities. A new Collaboratory was introduced. Brain Simulation Platform use increased and new tools were added for modelling at different biological scales, The HPAC Platform has developed data federation and data-intensive computing services, such as the Fenix Data Transfer Service and Central Data Location Service and improved simulation tools’ readiness for HPC systems. The Medical Informatics Platform is deployed in 30 hospitals, with 20,000 datasets in dementia, mental health, epilepsy and traumatic brain injury – a scale offering statistical significance. The Neuromorphic Computing Platform unveiled a one million-core SpiNNaker system (the largest-ever neuromorphic platform) and supported learning and motor control loop experiments, plus application of structural plasticity to networks processing auditory and visual stimuli. The Neurorobotics Platform improved its usability and interoperability with other EBRAINS services, including HPC deployment, and supported spinal neurorehabilitation work, with publications in Nature and Nature Neuroscience.
The Grant Agreement Preparation Phase for SGA3 has been finalised. In SGA3, the HBP will focus on key scientific showcases and key elements of the EBRAINS RI. The EBRAINS AISBL has been created and a CEO hired; it is now building capacity to take over from EPFL as HBP Coordinator. The old Scientific Advisory Board and Clinical Advisory Board merged into a Science and Infrastructure Advisory Board. Nine Calls for Expression of Interest, to bring in new Partners, and Infrastructure Voucher Calls to support Partnering Projects, helped prepare for SGA3. The HBP developed a proposal for EBRAINS to join the European Strategy Forum on Research Infrastructures (ESFRI) Roadmap, to ensure its availability after the end of the FET Flagship.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The Virtual Epileptic Patient took an important step with the start of a first clinical trial in France, to improve surgical outcomes for epilepsy patients. The Human Brain Atlas offers an unprecedented “window on the brain”, with its ability to “place” scientific findings in their topographical context. Structural complexity of neurons is better understood, notably for pyramidal and cerebellar granular cells. Mouse brain work led to a model of the striatum, which is key for motor control, and the human auditory cortex is now understood in much finer detail. Mathematical models of wave-like activity and assembly projections improve our ability to create generic models of spiking neuron networks. Work by CDP6 within the Project led to the filing of three patents related to improving drug target identification.
The launch of EBRAINS makes available a first web portal providing access to services for brain research and brain-inspired sciences, helping scientists to collect, analyse, share and integrate brain data, and apply them to models and simulations. Interoperability between platforms is key; connecting the Knowledge Graph, Brain Simulation Platform and Neurorobotics Platform allows brain models to be imported in SONATA format for use in robotic experiments. Exploitation of neuromorphic computing systems in neurorobotics is also promising. Integration of The Virtual Brain into the HBP ecosystem boosted infrastructure capabilities. The number of formal Partnering Projects increased from seven at the end of SGA1 to 40.
Communications and dissemination included the HBP Museum Programme’s first interactive exhibition, promotion of HBP at INCF, SfN, and the HBP Summit/Open Day. The Education Programme showed how to apply HPAC to advance neuroscience and, with Ethics and Society experts, provided training in responsible research and innovation. The HBP also maintained its thought leadership, with journal articles such as “The Scientific Case for Brain Simulations” (Neuron) and the HBP’s “Synergy between neuroscience, computing, informatics, and brain-inspired technologies” (PLOS Biology). The Brain Simulation Platform produced an innovative outreach tool in its “Live Papers”, on line resources which combine texts describing work done with the datasets and software used to obtain the published results.

SP2: High-resolution fibre reconstruction using 3 different imaging techniques on one brain sample.

SP7: Left: HBP supercomputing centres (l) & model of hippocampus, visualized with ViSimpl (r).

SP1: Research at molecular, subcellular, cellular and whole brain level research in rodent and human

SP9 (a): The current, second-generation BrainScaleS microchip on its printed circuit board.

SP9 (b): The layout of the JIB-2 (SpiNNaker-2 prototype) chip, taped out at the end of SGA2.

SP9 (c): The JIB-1 (early SpiNNaker-2 prototype chip) test board, incorporating 4 JIB-1 chips.

SP10: A functional brain model simulated in the NRP controls a musculoskeletal body.

SP8 (b): Medical Informatics Platform showing datasets (l) & selected experiment variables (r).

SP4: SP4: Multiple scales & associated models investigated: somatosensory (barrel) cortex example.

SP8 (a): Kaplan-Meier estimator, used to estimate the survival function for longitudinal data.

SP5: Researchers can share, find and re-use multiscale neuroscience data via EBRAINS.

SP12 Ethics and Society: social and philosophical research, public engagement & ethics support.

SP6: Detailed models of 3 somatosensory neurons & their reduced models using Neuron_Reduce.