Accelerate Your Neuroscience Research with EBRAINS

EBRAINS tutorials and users day - 12 March 2025 in Heidelberg (Germany)

The EBRAINS tutorials and users day is for two audiences: newcomers to the EBRAINS Research Infrastructure (introductions, overviews, beginner hands-on tutorials) and seasoned EBRAINS users for advanced tutorials and user discussion groups with developers.

• Quick demonstration of a sample set of "EBRAINS science tools in action" in the morning plenary talks (this part of the event can also be attended online free of charge)
• Followed by parallel hands-on tutorials: meeting participants can attend 3 consecutive sessions and choose for each from a set of in parallel tutorials. This part is onsite only for most tutorials.
  
  

Registration

• for attending on-site in Heidelberg (Germany) -- registration fee (coffee breaks, catering lunch and dinner at the meeting site, ...): 40 Euro for student attendants (Bachelor, Master, PhD students) / 80 Euro for everybody else.
  • Non-project members:
    • We strongly recommend to register with an EBRAINS account, as the account gives access to the services presented and an account will be needed to use the EBRAINS RI hands-on
      • get an EBRAINS account HERE (free of charge)
      • then register with EBRAINS account (with registration fee for the meeting)
    • It is also possible to register without an EBRAINS account (use this option primarily, if your email domain is not (yet) on the positive-list for immediate EBRAINS account creation)
  • EBRAINS2.0 project members please register here
    
    
• for attending on-line (via zoom) to (only) the plenary talks, i.e. the part until 11:00h -- free of charge:
  • register for on-line attendance with EBRAINS account (recommended)
  • or register for on-line attendance without EBRAINS account

Venue

European Institute for Neuromorphic Computing (EINC),
Im Neuenheimer Feld 225a,
D-69120 Heidelberg,
Germany

Airports

• Nearest airport: Frankfurt international airport (FRA)
  • Train Station in the airport itself: Frankfurt Flughafen Fernbahnhof (use bahn.de for time table information)
  • About an hour by car. Info: we often used the TLS shuttle service in the past. A shuttle for up to 7 people costs around 160 Euro single trip. This shuttle needs to be booked in advance.
• also relatively close: Stuttgart airport (STR) Train station in the airport: "Stuttgart Flughafen/Messe". (use bahn.de for time table information)

Train station

Heidelberg Main Station (Heidelberg Hauptbahnhof, use bahn.de for time table information)

From Heidelberg Main station to the institute:

• 25 min walking distance
• or 5 min by tram (Tram number 24, direction: Handschuhsheim Burgstraße. The tram departs from "Steig E" outside the station building. See the plan of Heidelberg Main station.
  Leave the tram at "Bunsengymnasium", then walk 3 min to the institute)

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Time zone

The times in the agenda are in Central European Time CET (e.g. Europe, Berlin or Paris). Some other time zones: America, Australia, Europe, Japan, China, India)

(Only) the plenary talks can also be attended online. The tutorials are on site hands-on tutorials.

A high level introduction for researchers into the possibilities, tools and workflows offered by the EBRAINS Research Infrastructure today = for immediate use in own research projects

Briefly showing some of the tools / services / hardware systems or software environment, which are part of the EBRAINS research infrastructure in action -- "teasers" for the tutorials, starting after the coffee break.

(In parallel, 9:40h-11h: Facility Hub and Local Service Provider Meeting in the Seminar room R00.222 (ground floor)). This event is dedicated to the discussion and finalization of the Position Paper on the role of the Local Service Providers (including Facility Hubs), focused on accessory services to EBRAINS and their economic sustainability.

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The EBRAINS Knowledge Graph:

• Documentation
• Search

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Note: there are also two specific NEST related tutorials offered (see below):

• NESTML tutorial
• NEST astrocyte module tutorial

Tutorial offered: a beginners online hands-on experience on using NEST Desktop for teaching

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Tutorials offered: Introductory level and Advanced level.
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Tutorials offered: Beginners level tutorial and a machine-learning methods related tutorial.

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We also offer full-length tutorials for these tools -- EBRAINS has more tools than short introduction talks fit into the morning...

Interactively build and optimize your own data-driven, biophysically detailed neuron model, via EBRAINS services and HPC facilities.

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URL - (more details will be added to the agenda)

NESTML is a domain-specific language for neuron and synapse models.

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(The L2L tutorial had unfortunately to be cancelled)

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Introductory level tutorial to the Brain Scaffold Builder (BSB), a component framework for network reconstrruction and simulations at multiple levels of detail

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Cobrawap (Collaborative Brain Wave Analysis Pipeline) [1,2] is an open-source, modular and customizable data analysis tool developed in the context of HBP/EBRAINS, with the aim of enabling standardized quantitative descriptions of cortical wave dynamics observed in heterogeneous data sources, both experimental and simulated. The tool intercepts the increasing demand expressed by the Neuroscience community for reusability and reproducibility, offering a software framework suitable for collecting generalized implementations of established methods and algorithms, and for embracing innovative procedures. Inspired by FAIR principles and leveraging the latest findings in software engineering, Cobrawap is structured as a collection of modular Python3 building blocks that can be flexibly arranged along sequential stages, implementing data processing steps and analysis methods, directed by workflow managers (Snakemake or CWL). This “Getting started” tutorial [3] provides an introductory exercise to Cobrawap users, i.e. people interested in applying solutions already implemented in the software, for the exemplary scientific use-case of imaging recordings from mouse cortex under anesthesia. The value of this exercise goes beyond obtaining results from this specific use-case, since it allows also for “learning by doing” how the Cobrawap approach has been set up, and thus how it can be exploited in other scientific use-cases. Therefore, hints and clues will be given to people interested in developing new functions, i.e. expanding the pipeline to intercept their investigation goals and fit to their data types.

Requirements for attendees: a personal laptop for installing the software and storing test datasets and results.

References

[1] https://github.com/NeuralEnsemble/cobrawap, https://cobrawap.readthedocs.io
[2] Gutzen, et al. (2024) DOI 10.1016/j.crmeth.2023.100681
[3] https://github.com/APE-group/hands_on_cobrawap

Acknowledgments

Research co-funded by: European Union’s Horizon Europe Programme under Specific Grant Agreement No. 101147319 (EBRAINS 2.0); European Commission NextGeneration EU (PNRR EBRAINS-Italy MUR-CUP-B51E22000150006).

A three-parted demonstration session:

• the Medical Informatics Platform (MIP) demonstration will showcase the data catalog, including available federations and datasets. It will also demonstrate a machine learning algorithm from a clinician’s or researcher’s perspective—allowing users to select variables, configure parameters, and view intuitive visualizations via a user-friendly intuitive interface.
• and the Human Intracerebral EEG Platform (HIP) demo will showcase the HIP, highlighting its ability to facilitate secure data sharing, enable work in a private space, and support collaborative projects with restricted access to participating centers. It will also demonstrate its capacity to work in a remote desktop environment without leaving any fingerprint on personal computers or hospital infrastructure.
• The Platform for Human Imaging (PHI) demo will showcase PHI, an innovative platform developed from the HIP. Designed for storing, processing, and analyzing structural, functional, and diffusion MRI data, PHI is a fully remote system that provides a flexible working environment. Users can either develop code using a Bash terminal or take advantage of the user-friendly, intuitive applications integrated into the platform.

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Presenters: Lorenzo PINI and Paolo Emilio Mazzon (UNIPD)

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EBRAINS tools for teaching brochure and overview poster

Info: The tool inroduction talks of this tutorial can also be attended online or on-site free of charge . Please find the info and registration for this option here. Special invitation letters for teachers to this session in English and in German.

Tool tutorial registrations will be collected in the registration step. We will then distribute the hands-on tutorials to the 3 parallel slots to maximize the possibility for attendants to visit their preferred tool tutorials.