EBRAINS users days - Agenda

(show all abstracts)
(Agenda as of 2026/10/07-02:02 CEST)
Tuesday, 6 October 2026
08:45
EBRAINS users days -day I: especially for EBRAINS newcomers

We recommend to attend "in person" in Heidelberg. For people, who can not make it: The talks during the introduction day (6 October) will also be streamed (free of charge) via zoom. Please register here for attending via zoom online stream.

Venue: at the EINC in Heidelberg, Germany

Street address: Im Neuenheimer Feld 225a, 69120 Heidelberg, Germany.
Please see the EINC page for tram and parking info.

show a map of the venue (A few hotels are marked in the map with direct links to their own or their booking.com page. Heidelberg has a lot more hotels - listed e.g. on booking.com or on hrs.de)



Registration

The registration fee of 25 Euro / day includes the lunch at Heidelberg University mensa, coffee breaks and cookies.
To register for the users day:

(To request a free-of-charge EBRAINS users account please use https://ebrains.eu/register)

The registration deadline for on-site-attendance is Thursday, 1 October 2026
Until the meeting on 6 October you can still register for attending via zoom online stream -- see above for the URL


Posters

12 poster boards in the coffee break area are available (contact Björn to reserve one) to highlight tools or services and serve as conversation-starters:

  • The EBRAINS Software Distribution (ESD)
  • BrainScaleS neuromorphic compute system
  • EBRAINS tools-for-teaching
  • Clinical Connectome
  • 5M Connectome
  • In-depth metadata in the KG - enabling data reuse




(for linking to the agenda this ebrains.eu URL can be used.) .

08:45‑09:00
(15 min)		 Registration desk open

Collect your name-tag and a cookie.

09:00‑09:10
(10 min)		 Welcome to the dayKatrin Amunts
09:10‑10:00
(50 min)		 EBRAINS Research Infrastructure Introduction
  • Jan Bjaalie: An introduction tour through the whole EBRAINS Research Infrastructure
  • Boris Orth: The cloud, storage and HPC infrastructure powering EBRAINS
Moderated by Jan Bjaalie
10:00‑10:25
(25 min)		 Coffee break
10:25‑10:30
(5 min)		 Group photo
10:30‑11:30
(60 min)		 EBRAINS Data and Knowledge services: past, present, future

Introduction + panel discussion with audience feedback

Panelists :

  • Andrew Davison
  • Eszter Papp
  • Amaryllis Raouzaiou
  • Oliver Schmid
Moderated by
Jan Bjaalie
11:30‑12:30
(60 min)		 Lunch at Heidelberg University mensa

12:30‑12:45
(15 min)		 Introduction to the EBRAINS and Instruct-ERIC strategic collaborationKatrin Amunts
12:45‑13:05
(20+5 min)		 Instruct-ERIC: Get Funded Access to Advanced Technologies for Structural Biology Research

Instruct-ERIC is a pan-European distributed research infrastructure making high-end technologies and methods in structural biology available to users. In July, EBRAINS and Instruct-ERIC signed a Memorandum of Understanding, establishing a strategic collaboration to strengthen links between digital neuroscience and structural biology research infrastructures in Europe.

Regina Guenster (Instruct-ERIC)
13:10
Introduction to the basics of the EBRAINS Research Infrastructure
13:10‑13:55
(45+5 min)		 Session

An introduction to the core platform services of the EBRAINS research infrastructure, highlighting its shared workspaces, storage solutions, and interactive computing environments.

show abstract

Eleni Mathioulaki
and
Nikos Georgomanolis
14:00‑14:30
(30 min)		 Coffee break

14:30
Introductions to different aspects of the EBRAINS RI
14:30‑14:45
(15+5 min)		 Curation-Ready: Data, Models & Software

An introduction on how to prepare for curation of datasets, models or software for inclusion in the EBRAINS RI knowledge graph and data sharing services

Signy Benediktsdottir
14:50‑15:05
(15+5 min)		 Computing big: High Performance Compute (HPC) resources

Introduction of the ways the EBRAINS team can help creating a sound proposal for applying for High Performance Compute (HPC) resources for research cases, where local compute power is insufficient.

Ekaterina Zossimova (juelich)
15:10‑15:25
(15+5 min)		 The EBRAINS software distribution (ESD)

The EBRAINS software distribution provides a software environment (container) for using lots of EBRAINS tools in the same setup - from usage on an individual system up to HPC environments. This session demonstrates the process (download, use, scale up).

Eleni Mathioulaki
15:30‑15:45
(15+5 min)		 EBRAINS workflows: all tools on deck

Workflows combining different tools potentially running at different sites (e.g. for accessing local data sets and leverage compute power).

Ekaterina Zossimova (juelich)
15:50‑16:10
(20+5 min)		 Medical Analytics platforms
  • Platforms overview
  • Introduction to the PHI-Platform for Human Imaging
Alessandra Bertoldo (UNIPD)
16:15‑16:35
(20+5 min)		 High-level intro of the Medical Informatics Platform (MIP) and the Human Intracerebral EEG Platform (HIP)Evita Mailli and Viktoria Bastic Schmid
16:40‑17:00
(20+5 min)		 Cerebellar models repo and Cerebellar-hub

Workflows introductions to the cerebellar models repo and the Cerebellar-hub

Dimitri RODARIE (epfl)

Wednesday, 7 October 2026
09:00
EBRAINS user days - day II: hands-on tool tutorials

There slots, 2h each, of parallel offers for hands-on tutorials.

For most of the EBRAINS tools used in the tutorials an EBRAINS account will be needed. Best get your account ahead of time. If that is not possible you can also get a guest account on the spot to be able to participate in the hands-on tool usage sessions.

09:00‑09:15
(15 min)		 (Registration for attendants of day II)
09:15‑09:30
(15 min)		 Get your EBRAINS account ready -- guest accounts for the rest
09:30‑11:30
(120 min)		 Parallel hands-on tutorials

Medical Informatics Platform (MIP)

In this tutorial, participants will explore the Medical Informatics Platform (MIP), a federated research environment that enables secure discovery and analysis of distributed health data across institutions. Using the Public MIP instance, participants will gain an overview of the platform's architecture, learn about the principles of federated data sharing and analysis, and discover how researchers can access and work with available datasets through the MIP ecosystem. After a short introduction to the platform and its federated setup, participants will be guided through the data catalogue, the newly developed user interface, and a prepared analysis workflow. This hands-on session will provide practical insights into how the platform supports collaborative medical research while maintaining data sovereignty and privacy.

  • Each participant will have the opportunity to follow the prepared tutorial and explore the platform's capabilities directly. Participants will use the Public MIP instance and require an EBRAINS account (available free of charge at https://ebrains.eu/register) to access the platform and the tutorial datasets.
  • The tutorial will be conducted entirely through the MIP web interface, and participants only need a web browser on their own laptop.



The Virtual Brain (TVB) - introduction

The TVB session will be showing the basing building block of TVB, how to set up and run a whole-brain simulation, explained through use-cases of modeling epileptic seizures, virtual resection and stimulation. (See here for additional information)



SpiNNaker

In this tutorial, participants will learn how to access and use SpiNNaker, one of the world's largest neuromorphic computing platforms. After an initial introduction to the platform and the PyNN language on SpiNNaker, the participants will then be able to access the EBRAINS Jupyter Lab using a web browser on a laptop (a mobile phone is not recommended for this) and use this to follow exercises allowing them to build up their knowledge of running PyNN scripts on SpiNNaker. The workshop leader will be on hand throughout the session to help with any problems, and to answer any additional questions about the system and its use.

  • Participants can use their EBRAINS account (available at https://ebrains.eu/register free of charge) or can use a guest account during the tutorial. With an own account the participants can continue using the neuromorphic compute systems also after the end of the tutorial.

Knowledge Graph for data consumers

Description pending

Medical Informatics Platform (MIP)TVB - introductionHands-on SpiNNakerKnowledge Graph for data consumers Brain Scaffold Builder (BSB)
Georges Melissargos, Pauline Ducouret, Evita Maili and Kostas Filippopolitis


Room: Seminar room second floor R02.240

This tutorial introduces participants to the Medical Informatics Platform (MIP), a federated environment for secure discovery and analysis of distributed health data.

more info

Spase Petkoski


Room: Foyer on ground floor

The Virtual Brain (TVB) session showing the basic building block of TVB.

more info

Andrew Rowley


Room: Seminar room ground floor R00.222

Tutorial for the digital real time neuromorphic compute system SpiNNaker-1

more info

Raphaël Gazzotti, Oliver Schmid, Alix Bonard, Laura Morel, Andrew Davison


Room: Seminar room thrid floor R03.128 ("Oberstübchen")

If you would like to use the datasets, atlases, computational models or any other information in the EBRAINS Knowledge Graph, either in your research or in developing software tools, this tutorial will give hands-on demonstrations of the different tools available to you for both web-based and programmatic access. We will cover data organization with openMINDS, the KG Search UI, the Query Builder, the Neural Activity Resource and the fairgraph Python library, with case studies of analysing public datasets in the EBRAINS Lab and building a simple web app to visualise KG metadata.

Dimitri Rodarie (UNIPV)


Room: Seminar room thrid floor R03.240

The BSB is a framework for reconstructing and simulating multi-paradigm neuronal network models.
11:30‑12:30
(60 min)		 Lunch
12:30‑14:30
(120 min)		 Parallel hands-on tutorials

show abstract

Siibra-python in action: Advanced workflows with siibra-pythonTVB - resting state modellingIntegrated visual simulation and analysis workflows using NEST Desktop and Elephant LabKnowledge Graph for data providersEBRAINS demonstrators: Sensorimotor neurocontroller and Epileptic virtual brains5M Connectome Tutorial
Xiao Gui


Room: Seminar room first floor R01.240

The siibra toolsuite provides programmatic access to the EBRAINS multilevel brain atlas, integrating reference spaces, parcellation maps, and a broad range of multimodal neuroscience data. In this advanced, hands-on tutorial, participants will learn how to use siibra-python to integrate and analyse their own data in an atlas context.

more info

Spase Petkoski


Room: Seminar room second floor R02.240

This second TVB session will describe fast back-end implementation of the Montbrio-Pazo-Roxin model used for modeling resting state fMRI . This is a based on a more detailed showcase Degeneracy in neuroscience, as well as virtual brains with neuromodulation through the example of dopaminergic activity DOI 10.25493/9KR4-BNK

Cristiano Köhler, Tobias Michels and Michael Denker


Room: Foyer on ground floor

Introductory level tutorial introducing participants to analyzing electrophysiological data from simulation and experiment.

more info

Raphaël Gazzotti, Oliver Schmid, Alix Bonard, Laura Morel, Signy Benediktsdottir, Eszter Papp, Andrew Davison


Room: Seminar room ground floor R00.222

If you would like to share your experimental data, computational models, software, data from simulations, or data analysis results using the EBRAINS RI, this tutorial will explain the openMINDS metadata schemas and give hands-on demonstrations of the different tools available to you for both web-based and programmatic access. We will cover the KG Editor app, Collaboratory Bucket storage, the Metadata Wizard, the fairgraph Python library, and the bids2openminds command-line tool. You will learn how to share publicly and how to restrict access to your collaborators.

Cecilia Assolito (UNIPV) and Huifang Wang (AMU)


Room: Seminar room thrid floor R03.128 ("Oberstübchen")

Embodiment of brain-regions-inspired networks in sensorimotor learning and Virtual brain twins in epilepsy for personalized diagnosis and treatment

more info

Massimiliano Facca, Anna Ridolfo and Claudia Tarricone


Room: Seminar room third floor R03.240

Participants will become familiar with the 5M Connectome features, learn how to harmonize data across sites, and integrate different modalities, guided by an example research question.

more info
14:30‑15:00
(30 min)		 Coffee break
15:00‑17:00
(120 min)		 Parallel hands-on tutorials

More information about the tutorials in this slot:

show abstract

Introduction to simulating neural networks using ArborHands-on BrainScaleSHuman Intracerebral EEG Platform (HIP) powered by CHORUSCuration Q & A Large-Scale Simulation-Based Inference with TVB.Clinical Connectome Tutorial

Thorsten Hater


Room: Seminar room first floor R01.240

Target audience: Researchers interested in detailed cell models

This tutorial will show the basics of designing detailed cell models, how to run them using Arbor, and how to grow them into larger networks. more info

Room: Seminar room ground floor R00.222

ntro: Yannik Stradmann

In this tutorial, participants have the chance to explore BrainScaleS-2, one of the world’s most advanced analog platforms for neuromorphic computing. more info

Viktoria Bastic Schmid, Jonathan Haab and Florian Sipp


Room: Seminar room thrid floor R03.128 ("Oberstübchen")

This tutorial introduces participants to CHORUS, a trusted research environment for secure and collaborative data-driven research. more info


Room: Seminar room third floor R03.240

This is mainly intended as a Questions & Answers session, where data-providers can bring their issues/requests and discuss them on-site with curation team members.

Michiel van der Vlag


Room: Foyer on ground floor

This hands-on tutorial introduces large-scale Simulation-Based Inference (SBI) with The Virtual Brain (TVB) using a pre-built workflow hosted and accessible through the EBRAINS infrastructure register forthis part



more info

Andreea Stefania Radu (UNIPD)


Room: Seminar room second floor R02.240


Aim: Participants will become familiar with the Clinical Connectome features and will learn how to combine them to address a simple clinical research question.

more info
17:00
End of the hands-on tools trainings



Infos: