EBRAINS users days - Agenda

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.

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:

• if you have an EBRAINS account (recommended) please register here with EBRAINS account
• else (i.e. if you do not (yet) have an EBRAINS account), please register here

(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.) .

Collect your name-tag and a cookie.

• Jan Bjaalie: An introduction tour through the whole EBRAINS Research Infrastructure
• Boris Orth: The cloud, storage and HPC infrastructure powering EBRAINS

Introduction + panel discussion with audience feedback

Panelists :

• Andrew Davison
• Eszter Papp
• Amaryllis Raouzaiou
• Oliver Schmid

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.

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

The presentation covers

• account setup
• project workspaces using the Collaboratory Wiki, and file management via EBRAINS Drive and Data Proxy.
• a demonstration of interactive computing in EBRAINS Lab, featuring zero-installation Python notebook workflows and pre-installed tools from the EBRAINS Software Distribution across various research domains.
• the EBRAINS Handbook, documentation structured on the Diátaxis framework with multi-source search across the ecosystem.
• EBRAINS Forms, privacy-first and fully branded, with no third-party trackers and native integration into EBRAINS platform services - IAM, Data Proxy, GitLab and more.
• the TRL application, tracking service maturity from first evidence to a shareable badge.

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

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.

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).

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

• Platforms overview
• Introduction to the PHI-Platform for Human Imaging

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

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.

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

Siibra-python in action

Advanced workflows with siibra-python - Bring your own data (by Dr. Ahmet Nihat Simsek & Dr. Xiaoyun Gui)

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. Following a Bring Your Own Data approach, participants are encouraged to work with NIfTI images, such as fMRI activation maps, or sets of spatial coordinates. Example datasets will be provided for participants who do not bring their own data. The tutorial will cover advanced workflows for anatomical assignment and spatial analysis, including the probabilistic assignment of participant data to cytoarchitectonic brain regions and its integration with multimodal information available through EBRAINS, such as receptor densities, connectivity, cellular and microstructural data, and high-resolution BigBrain data. Participants will learn how to use siibra-python to place their own data into an anatomical context and combine it with multimodal information from the EBRAINS multilevel brain atlas.

Recommended preparation: Basic experience with Python/Jupyter is recommended. Participants wishing to bring their own data should provide NIfTI images or spatial coordinates in MNI152/ICBM152 space.

Integrated visual simulation and analysis workflows using NEST Desktop and Elephant Lab

In this introductory level tutorial we will introduce participants to analyzing electrophysiological data from simulation and experiment using the tools

• Neo (https://neuralensemble.org/neo) for representing and handling the data, and
• Elephant (https://python-elephant.org) for performing the actual analysis.

We will cover using the basic data objects, loading realistic datasets and performing analysis protocols using a novel intuitive interface (Elephant Lab). In addition, we will demonstrate how to prototype a spiking neuronal network simulation using the NEST Desktop graphical tool, transfer the simulation to the EBRAINS Jupyter environment, and analyze the simulation output in Elephant Lab. For the tutorial, participants will be able to follow the tutorial using the EBRAINS Collaboratory.

EBRAINS demonstrators: Sensorimotor neurocontroller and Epileptic virtual brains

• The " sensorimotor neurocontroller" workflow will show how spiking neural networks interact with embodied physics, and how cerebellar plasticity models can be tested in closed-loop conditions, with planner, motor cortex and sensory feedback. We will show this sensorimotor control system in multiple trials of reaching, exploring multiple target object positions and multiple perturbation forces, to define quantitative relationships with the performance accuracy along trials. Please find more details and an architecture description of the Sensorimotor neurocontroller here
• The " Epileptic virtual brains" workflow will show how stimulation impacts in epilepsy, by interfacing the epileptogenic zone network with electrode field calculations,in high-resolution whole-brain simulation (TVB)

5M Connectome Tutorial

The tutorial starts with a brief recap of the feature download process covered in the PHI tutorial, together with a walkthrough of the feature data directory structure, what is available and how it is organized. Participants then download, via the notebook, a subsample of 5M features. This is followed by a demonstration of a typical harmonization workflow using ComBat, to correct for site and scanner effects across the multicentric dataset. Finally, a worked example shows multimodal integration, combining features from different modalities (EEG, MRI, PET) around a sample scientific question, to illustrate how harmonized multimodal data can be used in an actual analysis.

The parallel tutorials

More information about the tutorials in this slot:

Introduction to simulating neural networks using Arbor

Arbor is a library for simulating biophysically detailed neuron models on modern hardware. It comes with a friendly Python interface hiding its blazingly fast C++ core; scaling from laptops to at least 4000 GPUs. In this tutorial, we will show you the basics of designing detailed cell models, how to run them using Arbor, and how to grow them into larger networks. We will demonstrate how to create data drive models using the Allen Brain Atlas as an example. Arbor is free and open-source software, developed in the Human Brain Project and EBRAINS.

BrainScaleS

In this tutorial, participants have the chance to explore BrainScaleS-2, one of the world’s most advanced analog platforms for neuromorphic computing. For the tutorial, participants will use a web browser on their own laptop for remote access to BrainScaleS-2 systems via the EBRAINS Research Infrastructure. After a short introduction to neuromorphic computing and spiking neural networks, they will learn how to express and run experiments on the neuromorphic platform through either the (machine-learning targeting) PyTorch- or the (neuroscience targeting) PyNN-based software interfaces. This will allow them to gain insights into the unique properties and challenges of analog computing and to exploit the versatility of the system by exploring user-defined learning rules. Each participant will have the opportunity to follow a prepared tutorial or branch-off and implement their own project on the systems.

• 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.
• For the tutorial we will use the non persistent quick start here on EBRAINS.
  
  

Human Intracerebral EEG Platform (HIP) powered by CHORUS

In this tutorial, participants will explore CHORUS, a trusted research environment that provides the tools and infrastructure needed to support secure, collaborative, and reproducible data-driven research. Designed to accommodate a wide range of scientific use cases, CHORUS enables researchers to manage and analyse diverse data types, including medical images and time series data within a unified collaborative workspace.

Using the Human Intracerebral EEG Platform (HIP) as a neuroscience-focused use case, participants will gain an overview of the platform’s capabilities and learn how to create workspaces, set up collaborative projects, and manage research activities across teams. They will be introduced to the CHORUS App Store, which provides access to a growing portfolio of analytical tools and services, and will learn how these can be integrated into their research workflows. Through a hands-on exercise with tutorial datasets, participants will create a project environment, organize resources, and take the first steps towards preparing and executing a simple analysis. This session will provide practical insights into how CHORUS supports collaborative research while ensuring secure and efficient data management.

• Participants will access the platform through a web browser on their own laptop.
• Participants will require an EBRAINS account (available free of charge at https://ebrains.eu/register) to access the platform and the tutorial datasets.
  
  

Large-Scale Simulation-Based Inference with TVB

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. Participants will learn how GPU-accelerated TVB simulations can be used as a large-scale simulator for likelihood-free inference, efficiently generating data across broad model parameter spaces. The tutorial demonstrates how these simulations are integrated into an SBI pipeline to learn relationships between model parameters and simulated observables and to estimate posterior parameter distributions. Particular attention is given to the computational advantages of GPU acceleration and how EBRAINS infrastructure can facilitate scalable and reproducible SBI workflows for computationally demanding whole-brain models.

Clinical Connectome Tutorial

Aim: Participants will become familiar with the Clinical Connectome features and will learn how to combine them to address a simple clinical research question. Structure: The tutorial opens with a short recap of how to request and download Clinical Connectome features within the CinecaPHI environment, followed by a walkthrough of the features directory structure. Participants then load a small subsample of patient data through the notebook and perform basic QC checks (e.g., visualizing lesion overlay on the template, checking surface reconstruction quality). Two guided activities illustrate how to work with these data around simple research questions: Lesion-based analysis: compute lesion volume and generate a lesion overlap map across the subsample, then relate lesion burden to a clinical outcome score with a simple correlation. Structure-connectivity comparison: compare cortical thickness and structural/functional connectivity between the lesioned and contralateral hemisphere, to show how to integrate features from different modalities in a single analysis

Parallel tutorial sessions:

Infos:

• On the day after the EBRAINS users days the education department of the EBRAINS 2.0 project organizes a students day Please find the agenda of the students day (8 October 2026). here
• If you want to experience another hands-on tutorial (only online, though): The "Virtual users days" happen from 12-14 October 2026