Virtual Users’ Week

Brain research requires access to core resources, such as imaging equipment, computing infrastructure, or clinical data. However, these resources are typically distributed across multiple institutions, creating fragmented workflows. As a modern researcher, your ability to collaborate with project partners is just as critical as your technical skills.

This workshop positions co-design as a core competency for the modern researcher. You will learn how to align diverse project partners, streamline fragmented processes, and apply FAIR principles to your research.

Target group of the workshop: This workshop is suitable for beginners and anyone who is interested in making their workflows interoperable with the EBRAINS research infrastructure

Expected learning outcomes: By the end of the workshop, participants will…

• have a better understanding of co-design and why it is valuable for brain research;
• learn about scientific use cases and demonstrators that were made interoperable with the EBRAINS research infrastructure through co-design;
• learn how to create workflow diagrams and communicate their research to other participants using co-design principles.

Preparations: Participants should register for an EBRAINS account.

Workshop Chair: Wouter Klijn, Forschungszentrum Jülich, Germany

Workshop Speakers: Dr Katya Zossimova, Forschungszentrum Jülich, Germany; Anastasiia Andriievska, RISE Research Institutes of Sweden

Bio: Katya has a PhD in Physics from the University of Exeter (UK), and was previously a scholar at the A*STAR Institute of High Performance Computing (Singapore) and the University of Freiburg (Germany). She is currently affiliated with the Simulation and Data Lab Neuroscience at Forschungszentrum Jülich, which is home to the fastest supercomputer in Europe. As a member of the EBRAINS Science Support team, she helps researchers to leverage the EBRAINS digital infrastructure and strives to make the latest computing technologies more accessible to the neuroscience community. She has been involved in several key initiatives related to co-design, student outreach, and the Google Summer of Code.

The online QUINT workflow is an analytical solution for rodent brain histology, allowing researchers to register brain section images to a reference brain atlas; and to extract, quantify and visualise labelled features in reference atlas space. It supports analysis using reference brain atlases from mouse and rat such as the Allen Mouse Brain Atlas Common Coordinate Framework version 3 (CCFv3) or the Waxholm Atlas of the Sprague Dawley rat version 4 (WHSv4).

Target group of the workshop: students and researchers working with 2D histological data and 3D light sheet microscopy.

Expected learning outcomes: What the QUINT Workflow is about, how to access the QUINT-online page and how to use it.

Preparations: none.

Workshop Speakers: Heidi Kleven, University of Oslo; Arda Balkir, University of Oslo; Cristina Martinez Gonzàlez, University of Edinburgh, and Maja A. Puchades, University of Oslo

This hands-on session introduces the siibra-explorer as the interactive gateway to the EBRAINS atlases across species (human, macaque, rat, mouse). We will navigate high-resolution reference templates and parcellations, compare atlas versions, and discuss how multimodal brain maps (ranging from cytoarchitectonic features to connectivity, images, and gene/gene-product information) are linked to regions of interest. Participants will learn practical workflows for locating regions, inspecting their context, and assembling publication-ready, shareable views. We will also touch on how the explorer connects to other EBRAINS resources to retrieve region-specific information for analysis and reporting. By the end, attendees will be able to confidently use siibra-explorer to interrogate brain organization across scales and modalities, and to communicate findings with clear, atlas-based visuals. The workshop is designed for first-time users and will include short, guided exercises and time for Q&A.

Target group of the workshop: Researchers and students in neuroimaging, neuroscience, and related fields who want to use atlas-based context in their work. No coding required. Basic familiarity with neuroanatomy and common reference spaces is helpful but not mandatory (beginner)

Expected learning outcomes: 

• Confident navigation of the siibra-explorer interface (search, atlas/parcellation selection, region analysis)
• Understanding of how atlas context supports analysis and reporting
• Exporting figures/screenshots suitable for presentations and publications (including quotations)

Preparations: 

• A laptop with a recent web browser (Chrome or Firefox recommended); a mouse is helpful.
• Stable internet connection.
• Create a free EBRAINS account in advance to enable saving/sharing where applicable.
• No prior attendance in another session required.

Workshop Speaker(s) / Tutor(s): TBC

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.

Target group of the workshop: Researchers interested in neuromorphic compute systems and emulating spiking neural networks (beginner).

Expected learning outcomes: Participants should gain insights into the unique properties and challenges of analog computing.

Preparations: Participants will need a computer with a web browser installed (in order to have access to the EBRAINS Lab) and an EBRAINS account or EBRAINS guest account.

Workshop Speaker(s): TBC

This workshop will give you an introduction to the million-core neuromorphic platform SpiNNaker and show you how you can access and use the platform yourself.  You will log in to the EBRAINS Jupyter lab, and from there write PyNN scripts to describe Spiking Neural Networks, which you will then run on SpiNNaker itself.  You will then be able to log in and go through some tutorials yourself with a SpiNNaker expert present.  You will also be able to ask questions of the expert to help you understand what might be possible now, and in the future.

Target group of the workshop: beginner

Expected learning outcomes: How to write PyNN SNN networks and run them on SpiNNaker via the EBRAINS Jupyter lab

Preparations: Participants will only need an EBRAINS account and a web browser (laptop / desktop recommended as Jupyter isn't easy to use on a mobile phone or tablet).

Workshop Speaker: Andrew Rowley, University of Manchester 

Bio: Andrew Rowley has worked as a Senior Research Software Engineer for the SpiNNaker platform since 2014, and has helped to allow easy access to the complex neuromorphic chips underneath to allow researchers to execute SNNs without having to understand those complexities.  Andrew originally gained his PhD in Artificial Intelligence from the University of St. Andrews where he worked on solving Quantified Boolean Formula, but has since been involved in many diverse software projects, from large scale video conferencing and lecture recording software, to text mining platform development at the National Centre for Text Mining.  In his role for SpiNNaker he also performs day-to-day management of the server infrastructure for the project which connects between EBRAINS and the systems hosted at the University of Manchester.  

Andrew Rowley presenting ''Hands on with Spinnaker''

NEST is an established open-source simulator for spiking neuronal networks that combines detailed biological modeling with high performance and scalability from laptops to HPC systems, and has supported hundreds of studies, including a large-scale model of human cortex. This tutorial takes the user through a practical NEST’s support for compartmental neuron models and advanced synaptic plasticity.

As an example of advanced plasticity rules in NEST, we present supervised eligibility propagation, an online, biologically inspired learning rule that approximates backpropagation through time. We show how this rule can be used to train functional spiking neural networks to learn a range of tasks, from which we highlight the classification and generation of handwritten characters. The tutorial covers the full research workflow from model construction and simulation to data analysis.

Target group of the workshop: Intermediate (some Python programming skills required)

Expected learning outcomes: Hands-on experience creating and analysing a spiking neural network simulation using NESTML and NEST Simulator. 

Preparations: No preparation needed.

Workshop Speaker: Charl Linssen, Jülich Research Centre, Jülich, Germany

Bio: Charl Linssen works as a Research Software Engineer on the NEST and NESTML spiking neural network simulation software at the Jülich Supercomputing Centre (Jülich, Germany).

Charl Linssen - NEST Simulator

This coding workshop introduces siibra-python, the programmatic interface to the EBRAINS atlases. We will explore how to query atlases across species, select parcellations, look up regions by name or coordinate, and retrieve linked multimodal data (e.g., maps, tables, and metadata) for analysis. Through guided notebooks, participants will learn practical workflows for integrating atlas context into Python-based pipelines, generating reproducible results, and exporting figures and data products for publications.

Target group of the workshop: Researchers, data scientists, and students who want to use Python to work with atlas-based information. (Intermediate)

• Prerequisites: Basic Python (variables, functions, packages) and familiarity with Jupyter notebooks.
• Helpful but not mandatory: Basic neuroimaging concepts (reference spaces, parcellations) and experience with packages such as nilearn.

Expected learning outcomes: 

• Install and set up siibra-python and navigate the core API.
• Select atlases/parcellations; find regions by name or MNI coordinates.
• Fetch region-linked data (e.g., probabilistic maps, annotations/metadata) and use them in analysis workflows.
• Produce shareable, reproducible notebooks and export publication-ready visuals.

Preparations: 

• Laptop with a recent browser and a local Python environment
• Pre-install (or be ready to install) the following: siibra, nilearn
• We will provide sample notebooks in advance
• Stable internet connection
• A free EBRAINS account for access to related services and to save/share materials where applicable.
• No prior attendance in another session required.

Workshop Speaker(s) / Tutor(s): TBC

This workshop offers inter- and transdisciplinary methods and tools for collaborative work on projects that can also be especially beneficial for virtual collaborations:

• The integration of various disciplines, thinking patterns, experiences and work styles.
• Procedures and Tools for appreciative collaboration in heterogenous teams.
• Fair work distribution, virtual decision-making and conflict resolution.

Methods: Trigger Talks on interdisciplinary collaboration, challenges and tools; break-out sessions for case studies; individual and group reflection.

Target group of the workshop: everyone interested in effective international research collaborations (all levels)

Expected learning outcomes: Recognising collaborative challenges routed in the interplay of different disciplines, locations, career aspirations, and cultures. Knowing tools that support a productive international research collaboration, specifically online.

Preparations: 

• Come with an open mind, interest in an open dialogue with colleagues and curiosity to check out some collaborative tools.
• A good internet-connection and quiet place to join the break-out sessions.

Workshop Chair: Dipl.-Ing. Dr.techn. Karin Grasenick

Workshop Speakers: Dr. Karin Grasenick, CONVELOP; Anna Saemisch M.A., CONVELOP

Bios:

Dr. Karin Grasenick bridges the worlds of science, technology, and equity. With academic roots in mathematics, computer science, and a PhD in biomedical engineering, she supports universities, funding bodies, and research initiatives, particularly former FAT flagship Human Brain Project and EBRAINS2.0). As the founder of CONVELOP and a long-standing partner of Graz University of Technology, her work focuses on developing practical tools, strategic guidelines, and training programs that help research teams integrate diversity as a core dimension of collaboration and scientific excellence.

Anna Saemisch, M.A., works at the intersection of education, innovation, human resources and social development. She studied psychology (Dresden University of Technology) and adult and continuing education (Karl-Franzens University of Graz). She combines empirical research with the design of practice-oriented solutions and draws on a broad repertoire of qualitative and quantitative methods, applying them in a targeted manner depending on the context.

The EBRAINS Knowledge Graph (KG) helps you to find and share the data, software and models you need to make your next discovery. You can:

• Search and use interesting data
• Manage and publish your metadata
• Collect metadata with queries
• Visualise the graph
• Access data programatically
• Organise and monitor your work
• Automate your processes

The KG also works together with EBRAINS tools.

Further information to be announced soon.

The HIP is an open-source platform dedicated to the collection, curation, sharing, and analysis of human intracerebral EEG (iEEG) data at international scale. Developed within the Human Brain Project and operational since 2022, it connects hospitals and research centers working on some of the rarest and most valuable data in neuroscience: recordings collected directly from the human brain.

The Medical Informatics Platform (MIP) is designed to help clinicians, clinical scientists, and clinical data scientists aiming to adopt advanced analytics for clinical research. Users can explore harmonized medical data extracted from pre-processed neuroimaging, neurophysiological and medical records and research cohort datasets without transferring original clinical data.

Further details to be announced soon.

The Virtual Brain (TVB) is an open-source platform for constructing and simulating personalised brain network models. The TVB-on-EBRAINS ecosystem includes a variety of prepackaged modules, integrated simulation tools, pipelines and data sets for easy and immediate use on EBRAINS. Process your large cohort databases and use these results to develop potential medical treatments, therapies or diagnostic procedures.

Further details to be announced soon.

This workshop introduces tvb-ext-xircuits, a JupyterLab extension that enables users to visually create and execute workflows based on The Virtual Brain (TVB) and related tools within the EBRAINS Lab environment.

The first part of the workshop will provide a short introduction to key TVB concepts, such as brain connectivity, models, simulations, and their main building blocks, to give participants the necessary context before exploring the xircuits extension.

Participants will explore existing workflows for running TVB simulations and Virtual Brain Inference (VBI) workflows using a visual, component-based interface. The workshop will demonstrate how complex computational workflows can be represented as connected components, making them easier to understand, configure, and reuse.

Participants will also be introduced to the possibility of extending these workflows by creating new Xircuits components directly within EBRAINS Lab. 

Target group of the workshop: The workshop is intended for beginner to intermediate users, who are interested in computational neuroscience and brain modelling.

Expected learning outcomes:
By the end of the workshop, participants will be able to:

• understand the purpose of tvb-ext-xircuits and how it integrates with EBRAINS Lab;
• understand how a computational workflow can be represented visually using
• interconnected components;
• explore and execute existing Xircuits workflows based on TVB and VBI;
• modify workflow parameters and understand how information is passed between components;
• understand how Xircuits workflows can be extended with new components;
• create a simple custom Xircuits component directly within EBRAINS Lab and use it in a workflow.

Preparations:
Participants do not need to install software locally, as the workshop will be carried out entirely within EBRAINS Lab.
For the workshop, participants should:

• have an active EBRAINS account;
• make sure they can access EBRAINS Lab;
• have attended, or be familiar with the basic concepts presented in the preceding introductory workshop on The Virtual Brain.
• No advanced programming preparation is required. Basic familiarity with Python may be helpful for the component-creation exercise, but the necessary concepts will be explained during the session.

Workshop Speakers: Paula Prodan, CODEMART; Lia Domide, CODEMART

Bios:
 

Lia Domide: Codemart, Romania

Lia Domide: Codemart - Romania
Software engineer of TVB (The Virtual Brain), working with professional standards in neuroscience EU founded projects, for co-designing with researchers good solutions for brain twin models.

Paula Prodan - Codemart, Romania

Paula Prodan: Codemart - Romania

Software developer with a strong focus on scientific software projects. She has contributed to the core The Virtual Brain (TVB) application, helped automate the preprocessing pipeline in its early stages, and briefly worked on the inversion pipelines.