Get access to the state-of-the-art facilities and resources of HBP partner institutions, to foster collaboration and carry out cutting-edge scientific research.

HBP and HBP partners provide access to three types of Facility Hubs:

  1. Physical facilities (e.g. microscopes)
  2. Competence centres providing specialized software support going beyond the EBRAINS High Level Support Team
  3. The European Institute for Theoretical Neuroscience (EITN)

Facility Hubs are aligned with the FENIX supercomputing network to provide user access to computing resources, e.g. for data storage, analysis, and simulation.

The first Facility Hub pilots will be operational by the end of March 2021. Additional Hubs are planned to follow.

The Facility Hubs are contributions from HBP partners to the new EBRAINS research infrastructure, and complement the EBRAINS services currently on offer.
 

 

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Access and Terms of Use

Users from academia and industry world-wide are eligible to apply for access to HBP Facility Hubs.

Getting access:

  • Interested users of the Facility Hubs are asked to contact the respective Facility Hub contact for a first discussion on the potential project and support as well as the feasibility. Users must bring their own funding for the project which goes beyond the offer/support by the Facility Hub. Facility Hub support can also be included in applications to calls. 
  • Users are asked to submit a short project description to the Facility Hub contact using the template provided by the Facility Hub contact, which includes a project summary, complementarities and synergies with the Human Brain project, and the expected outputs. Since most of the Facility Hubs require extensive compute resources (e.g. for simulations or data storage), the Facility Hubs are aligned with the Fenix research infrastructure. Facility Hubs have applied via ICEI (Interactive Computing E-Infrastructure for the Human Brain Project) for a certain amount of compute and data, resources which they can make available via "wide access" to users of the hub. If users would need more resources than supplied at the Hubs, they would have to submit a request via ICEI.
  • The respective Facility Hub decides which projects are supported according to its rules and regulations. Criteria for the selection are scientific excellence, impact and contribution to the aims of the Human Brain Project, EBRAINS and the Facility Hub, as well as ethical compliance with the regulations of the Hub.
  • Before the project starts, a Usage Agreement is signed. The usage needs to be in agreement with the EBRAINS General Terms of Use and the EBRAINS Access Policy as well as with the Facility Hub-specific licence and rules. Results (e.g. datasets, software, models) need to be curated in EBRAINS and publications or other communications using results of the project need to acknowledge the Human Brain Project and EBRAINS (and the ICEI project, if any ICEI resources were used).
  • Supported projects are offered to become a Partnering Project of the HBP and to enjoy the benefits of an associated HBP Partner.

Reporting:

  • Users are asked to deliver a short project report by the end of the project according to the template which will be provided by the Facility Hub contact before the project start.

Monitoring:

  • To monitor the interest and usage of the Facility Hubs by the community, user requests and outcomes of supported projects are documented and analysed on a yearly basis. This information is only for internal use. Collected data is GDPR compliant.

Physical Facilities

Click on the individual hubs below to learn more.

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Two-photon imaging and ensemble recordings, both conducted in behaving, task-performing animal models, are illuminating our understanding of how cognitive, perceptual and motor functions originate from the behavior of large, cooperating populations of neurons. The University of Amsterdam (UvA) facility hub and competence center offers access to a Leica fast resonant two-photon scanner and high-density ensemble recording setups using Neuropixels and other silicon probe configurations. The core expertise in electrophysiological, optical and behavioral recordings is supplemented by opto- and chemogenetics, large-scale data analysis centered on population decoding and computational modelling.

The UvA can host medium (2-6 mo.) or longer (>6 mo.) term projects for PhD students, postdocs and research staff who need to acquire multiple technical skills and/or want to acquire data for a project. Shorter or remote visits are possible for researchers wanting to learn individual skills related to data-analysis. Organizing online and on-site courses and webinars for large groups is also possible.

The UvA harbours one of the largest groups for two-photon in vivo neuronal imaging and ensemble recordings in Europe, which is uniquely distinguished by its development of sophisticated behavioral paradigms testing multisensory perception, memory and consciousness, a high level of multidisciplinary integration and technical versatility.

Contact person: Paul Mertens, p.e.c.mertens@uva.nl

Additional information: Systems and Neuroscience Group web page

Competence Centres

Click on the individual hubs below to learn more.

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The HUB is based in UNIPV and performs multiscale modeling spanning from neurons and microcircuits to large-scale networks and the whole brain. The HUB leverages on the unique concept of the Brain Scaffold Builder (BSB), a modeling workflow that allows multiscale modeling of neurons, microcircuits, large-scale networks and whole brains.

Although initially designed for the cerebellum, BSB can be easily applied to any brain networks through customized developments on demand. The BSB supports different modeling platforms and formats and can be applied to neuromorphic hardware, robotic control systems and virtual brain simulators. A special aspect of the HUB is to provide the infrastructure and expertise for multiscale experimental validation of the models in rodents. The HUB is relying on EBRAINS and shares with it a set of highly integrated APIs and several sophisticated model building tools.

Dedicated community managers will help users through any issue they may have in exploiting the HUB, in arranging the specific development workflows and simulation of interest, or to help in getting the appropriate HPC allocation for the project. In summary, the HUB will allow researchers and customers with different interests, background, and expertise to develop their own computational models and transform them into different kinds of applications. Dedicated tutorials and community managers will guide users through all the steps needed to reach their specific goals.

The highest impact of this unique installation is expected on engineering and medicine, especially concerning brain-inspired technologies and the investigation and cure of brain diseases.

Contact person: Egidio D’Angelo, dangelo@unipv.it

Technical assistance: Simona Tritto (simona.tritto@unipv.it) and Stefano Masoli (stefano.masoli@unipv.it)

Additional information: https://dangelo.unipv.it/

 

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The Virtual Brain (TVB) is a full brain network simulation engine, which significantly reduces the gap between computational models and human brain imaging data. The TVB Facility Hub and competence center at Aix-Marseille University provides field-specific expert support for activities linked to the use of TVB (model building, simulation, analysis, validation and model inversion). Training is provided in TVB workshops and through internships. The TVB Facility Hub serves as the first point of contact for domain-specific questions and refers users to other HBP/EBRAINS groups for further assistance as appropriate.

Potential users: Students, post docs and researchers in neuroscience, as well as engineers in neurotechnology and clinicians.

Uniqueness: Field-specific expert performance in various domains (high-performance computing, simulation science, brain imaging, neuroscience) is integrated into complex workflows, enabling interoperability of tools within TVB and EBRAINS eco-system. TVB Facility Hub and competence center provides the user with support in building up an integrated understanding of TVB and adapting the workflows to the user’s own needs.

Impact: To increase the capacity of neuroscientists to use ICT tools such as TVB and EBRAINS to advance science and enable more efficient translation into clinical applications.

Contact: Viktor Jirsa, email: viktor.jirsa@univ-amu.fr

Links: https://ins-amu.fr , https://www.thevirtualbrain.org

Publications:

Sanz-Leon P, Knock SA, Woodman MM, Domide L, Mersmann J, McIntosh AR, Jirsa VK (2013) The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics 7:10. doi: 10.3389/fninf.2013.00010

Sanz-Leon P, Knock SA, Spiegler A, Jirsa VK (2015) Mathematical framework for large-scale brain network modelling in The Virtual Brain. Neuroimage 1;111:385-430. doi: 10.1016

Jirsa V., Woodman M.M., Domide L. (2021) The Virtual Brain (TVB): Simulation Environment for Large-Scale Brain Networks. In: Jaeger D., Jung R. (eds) Encyclopedia of Computational Neuroscience. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7320-6_100682-1