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EBRAINS tutorials and users day - Agenda

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Wednesday, 12 March 2025
08:20
EBRAINS tutorials and users day

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




Venue

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

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)

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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Option for participants with young children (age 1.5 -6 years)

We can book child care (for children age 1.5 to 6 years) at the universities KidsClub, 7 min walking distance from the meeting location. This option is (only) available until end of January (and only for children with both measles vaccinations completed). Please contact kindler@kip.uni-heidelberg.de for this option.

08:20‑08:50
(30 min)
 Registration
08:50
Plenary -- can also be visited online
08:50‑08:58
(8+2 min)
 Welcome to the meeting
09:00‑09:08
(8+2 min)
 Welcome to the EBRAINS tutorials and users day
09:10‑09:35
(25+5 min)
 Research with EBRAINS - a high level overview

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

Katrin Amunts (juelich)
09:40
Plenary: tools in action

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.

09:40‑09:45
(5+2 min)
 Science software environment: The EBRAINS software distribution (ESD)
09:47‑09:52
(5+2 min)
 Science tools in action: working with data from the EBRAINS Knowledge Graph

The EBRAINS Knowledge Graph:


Tutorials offered: Introductory, Extended and Advanced

show abstract

09:54‑09:59
(5+2 min)
 Science tools in action: Arbor, multicompartmental simulation library

Tutorial offered: Hands-on Introduction to Arbor for beginners
show abstract
10:01‑10:06
(5+2 min)
 Science tools in action: NEST Desktop

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

show abstract

10:08‑10:13
(5+2 min)
 Science tools in action: TVB (The Virtual Brain)

Tutorial offered: model building and simulation, inference
Spase Petkoski (amu)
10:15‑10:20
(5+2 min)
 Science tools in action: Neuromorphic compute system SpiNNaker

SpiNNaker is a highly programmable neuromorphic platform, designed to simulate large spiking neural networks in real-time. It uses many conventional low-power ARM processors executing customizable software in parallel, coupled with a specialized multicast network enabling the transmission of many spikes to multiple target neurons.

Tutorial offered: Beginners level tutorial. show abstract
Andrew Rowley (uman)
10:22‑10:27
(5+2 min)
 Science tools in action: QUINT workflow (workflow to support atlas-based quantification)

Tutorial offered: hands-on tutorial for beginners
show abstract
10:29‑10:34
(5+2 min)
 Science tool in action: tauRAMD (computation of relative residence times (τ) or dissociation rates of protein-ligand complexes) and SDA (Simulation of Diffusional Association)

Tutorial offered: Hands-on introduction

show abstract

10:36‑10:41
(5+2 min)
 Science tools in action: Snudda (building networks of neurons with synaptic connectivity based on the morphologies of reconstructed neurons and touch detection)


Tutorials offered: Introductory level and Advanced level.
show abstract

10:43‑10:48
(5+2 min)
 Science tool in action: Building reproducible workflows with EBRAINS atlases using siibra-python

Tutorial offered: siibra entry level
show abstract
10:50‑10:55
(5+2 min)
 Science tools in action: Neuromorphic Compute system BrainScaleS

BrainScaleS-2 is one of the world’s most versatile platforms for neuromorphic computing. Its software-controlled analog processing core emulates the dynamics of biological neurons and synapses to enable the exploration of spiking neural networks on a unique substrate.

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

Beginner level tutorial: In this tutorial, participants will get individual remote access to the BrainScaleS-2 platform. They will learn how to program the system, explore its analog properties and create spiking neural networks that learn to solve user-defined tasks. The session will be suitable for building basic knowledge about neuromorphic processors and analog computing as well as for kickstarting complex scientific research on BrainScaleS-2.

Machine learning methods related tutorial: Recent advances in machine learning with neural networks require an increasing energy budget. Neuromorphic hardware platforms, such as the BrainScaleS-2 (BSS-2) system, aim to offer accelerated energy-efficient computing solutions through analog computation. However, scalable training of spiking neural networks (SNNs) on an analog substrate remains challenging. Our jaxsnn software framework (based on JAX) enables data-efficient event-based gradient computation, tailored for optimizing networks on hardware operating on event data. In this hands-on tutorial, participants will first learn how to use jaxsnn on BrainScaleS for implementing “Spiking Heidelberg Digits” (SHD) spoken digit classification with a spiking neuronal network on the BSS-2 system.

10:57
And there is more...

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


 Tutorial offered: Hodgkin-Huxley Neuron Builder / Hippocampus Hub tools/web app

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

show abstract

Luca Leonardo Bologna (cnr)

 Tutorial offered: NEST astrocyte module tutorial

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


 Tutorial offered: NESTML tutorial

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

show abstract

Charl Linssen (juelich)

 Tutorial offered: Vast parameter space explorations using L2L on EBRAINS

This tutorial features a session on a hyper-parameter optimization framework, called L2L1, implementing the concept of learning to learn.
show abstract


 Tutorial offered: Using Neo and Elephant for the Analysis of Electrophysiological Data

show abstract


 Tutorial offered: EBRAINS tools for teaching

(This tutorial might be of interest also for science school teachers in grade 8 and above to determine, whether some 'real research tools' could also be used in their teaching setting) EBRAINS tools for teaching brochure and overview poster

show abstract

11:00‑11:30
(30 min)
Coffee break
11:30
Parallel sessions

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.

11:30‑13:00
(90 min)
 Hands-on tutorials in parallel
Hands-onHands-on Hands-onHands-onHands-on Users meeting






Facility Hubs representatives meeting
(TBC: facility hubs users as well?)

13:00‑13:50
(50 min)
 Lunch (catering in the institute)

(Optional during the lunch break: 15 min "European Institute for Neuromorphic Computing" building tour -- visit the BrainScaleS analog neuromorphic compute hardware system setup)
13:50‑14:00
(10 min)
 Group photo
14:00‑16:00
(120 min)
 Hands-on tutorials in parallel
Hands-on Hands-on Hands-on Hands-on




16:00‑16:30
(30 min)
 Coffee break
16:30‑18:30
(120 min)
 Hands-on tutorials in parallel
EBRAINS Tools for TeachingHand-on Hands-on Hands-on Hands-on





18:30‑19:50
(80 min)
 Dinner (catering at the institute) and get together

(Optional during the dinner break: 20 min "European Institute for Neuromorphic Computing" building tour -- visit the BrainScaleS analog neuromorphic compute hardware system setup)
19:50‑20:50
(60 min)
 (Optional: space and time for discussion groups)